Nextflow 24.04.4 is available - Please consider updating your version to it N E X T F L O W ~ version 22.10.8 Launching `main.nf` [comp-844c235b-1730-4312-8421-a74a883] DSL1 - revision: eb4a2cc2c0 [7c/23dd13] Submitted process > capsule_segmentation_preprocessing_1 (capsule-9114746) [capsule-9114746] cloning git repo... [capsule-9114746] running capsule... Paths in Data Directory: ../data/merscope_run/experiment.json ../data/merscope_run/polyt.png ../data/merscope_run/dapi.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif Arguments: --expt-path ../data/merscope_run/ --expt-region region_0 --section-subregion DAPI --model-path ../data/cellpose_model/CP_20240611_mousedev --pixel-size 0.108 --cell-diameter 10 --z-thickness 1.5 --n-planes 7 --max-tile-size 350 --min-transcripts 1000 subrgn evaluated: DAPI len(seg_pipeline.raw_spot_table)=16398139 Number of Tiles=53 Paths in Results Directory: ../results/detected_transcripts.csv.npz ../results/SegmentationPipeline.pkl ../results/seg_tiles/tile_0/run_spec.pkl ../results/seg_tiles/tile_1/run_spec.pkl ../results/seg_tiles/tile_2/run_spec.pkl ../results/seg_tiles/tile_3/run_spec.pkl ../results/seg_tiles/tile_4/run_spec.pkl ../results/seg_tiles/tile_5/run_spec.pkl ../results/seg_tiles/tile_6/run_spec.pkl ../results/seg_tiles/tile_7/run_spec.pkl ../results/seg_tiles/tile_8/run_spec.pkl ../results/seg_tiles/tile_9/run_spec.pkl ../results/seg_tiles/tile_10/run_spec.pkl ../results/seg_tiles/tile_11/run_spec.pkl ../results/seg_tiles/tile_12/run_spec.pkl ../results/seg_tiles/tile_13/run_spec.pkl ../results/seg_tiles/tile_14/run_spec.pkl ../results/seg_tiles/tile_15/run_spec.pkl ../results/seg_tiles/tile_16/run_spec.pkl ../results/seg_tiles/tile_17/run_spec.pkl ../results/seg_tiles/tile_18/run_spec.pkl ../results/seg_tiles/tile_19/run_spec.pkl ../results/seg_tiles/tile_20/run_spec.pkl ../results/seg_tiles/tile_21/run_spec.pkl ../results/seg_tiles/tile_22/run_spec.pkl ../results/seg_tiles/tile_23/run_spec.pkl ../results/seg_tiles/tile_24/run_spec.pkl ../results/seg_tiles/tile_25/run_spec.pkl ../results/seg_tiles/tile_26/run_spec.pkl ../results/seg_tiles/tile_27/run_spec.pkl ../results/seg_tiles/tile_28/run_spec.pkl ../results/seg_tiles/tile_29/run_spec.pkl ../results/seg_tiles/tile_30/run_spec.pkl ../results/seg_tiles/tile_31/run_spec.pkl ../results/seg_tiles/tile_32/run_spec.pkl ../results/seg_tiles/tile_33/run_spec.pkl ../results/seg_tiles/tile_34/run_spec.pkl ../results/seg_tiles/tile_35/run_spec.pkl ../results/seg_tiles/tile_36/run_spec.pkl ../results/seg_tiles/tile_37/run_spec.pkl ../results/seg_tiles/tile_38/run_spec.pkl ../results/seg_tiles/tile_39/run_spec.pkl ../results/seg_tiles/tile_40/run_spec.pkl ../results/seg_tiles/tile_41/run_spec.pkl ../results/seg_tiles/tile_42/run_spec.pkl ../results/seg_tiles/tile_43/run_spec.pkl ../results/seg_tiles/tile_44/run_spec.pkl ../results/seg_tiles/tile_45/run_spec.pkl ../results/seg_tiles/tile_46/run_spec.pkl ../results/seg_tiles/tile_47/run_spec.pkl ../results/seg_tiles/tile_48/run_spec.pkl ../results/seg_tiles/tile_49/run_spec.pkl ../results/seg_tiles/tile_50/run_spec.pkl ../results/seg_tiles/tile_51/run_spec.pkl ../results/seg_tiles/tile_52/run_spec.pkl [capsule-9114746] completed! [37/742f1a] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [fc/1ea31a] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [5c/787b29] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [b6/90fa13] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [eb/aaf24c] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [15/263fb6] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [4f/c5605a] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [f6/63023b] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [ba/4ddbbd] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [73/0009a8] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [ed/a2cf2e] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [26/587b9f] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [ae/657163] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [10/44f861] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [e2/31db59] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [82/940dd7] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [df/b98f4d] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [e8/a98a3e] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [a1/9c4f59] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [6a/2efa04] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [cd/1fbc63] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [b8/ce96c1] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [7e/b87ee3] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [2c/42000e] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [0d/bab613] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [e8/412014] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [bb/b9a7c3] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [be/c78d38] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [4f/2e60fc] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [80/ebec69] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [4a/2ee29c] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [0f/6b1406] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [c1/4c47b0] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [fb/b0f44f] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [80/c6cf88] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [c0/10c493] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [99/9519fd] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [39/466fad] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [8e/c3b3a8] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [a5/5dff60] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [e6/a0629a] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [60/c41ad3] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [89/36c6b4] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [e3/c3116b] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [17/00dd8f] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [75/878c1c] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [2d/f5ccf8] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [f0/dacb65] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [d4/a6e9b0] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [10/058363] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [d3/b0d161] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [f0/eb2c60] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/tile_1/run_spec.pkl ../data/merscope_run/experiment.json ../data/merscope_run/polyt.png ../data/merscope_run/dapi.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((1796.063528060913, 2123.172455469767), (3321.1534534801135, 3656.970969460227)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_1.npy'}) Paths in Results Directory: ../results/segmentation_result_1.npy [capsule-8021045] completed! [d9/993431] Submitted process > capsule_segmentation_run_2 (capsule-8021045) [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/tile_0/run_spec.pkl ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev ../data/merscope_run/experiment.json ../data/merscope_run/polyt.png ../data/merscope_run/dapi.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((1498.954600652059, 1826.0635280609133), (3321.1534534801135, 3656.970969460227)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_0.npy'}) Paths in Results Directory: ../results/segmentation_result_0.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/tile_12/run_spec.pkl ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((2093.1724554697676, 2420.2813828786216), (3932.788485440341, 4268.606001420455)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_12.npy'}) Paths in Results Directory: ../results/segmentation_result_12.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev ../data/tile_13/run_spec.pkl Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((2390.2813828786216, 2717.3903102874756), (3932.788485440341, 4268.606001420455)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_13.npy'}) Paths in Results Directory: ../results/segmentation_result_13.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/tile_14/run_spec.pkl ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((310.51889101664227, 637.6278184254965), (4238.606001420454, 4574.423517400568)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_14.npy'}) Paths in Results Directory: ../results/segmentation_result_14.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/merscope_run/experiment.json ../data/merscope_run/polyt.png ../data/merscope_run/dapi.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/tile_15/run_spec.pkl ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((607.6278184254965, 934.7367458343506), (4238.606001420454, 4574.423517400568)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_15.npy'}) Paths in Results Directory: ../results/segmentation_result_15.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/tile_2/run_spec.pkl ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((904.7367458343506, 1231.8456732432048), (3626.970969460227, 3962.7884854403405)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_2.npy'}) Paths in Results Directory: ../results/segmentation_result_2.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/tile_11/run_spec.pkl ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((1796.063528060913, 2123.172455469767), (3932.788485440341, 4268.606001420455)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_11.npy'}) Paths in Results Directory: ../results/segmentation_result_11.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev ../data/merscope_run/experiment.json ../data/merscope_run/polyt.png ../data/merscope_run/dapi.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/tile_10/run_spec.pkl Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((1498.954600652059, 1826.0635280609133), (3932.788485440341, 4268.606001420455)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_10.npy'}) Paths in Results Directory: ../results/segmentation_result_10.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/tile_21/run_spec.pkl ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((2390.2813828786216, 2717.3903102874756), (4238.606001420454, 4574.423517400568)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_21.npy'}) Paths in Results Directory: ../results/segmentation_result_21.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/tile_38/run_spec.pkl Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((2390.2813828786216, 2717.3903102874756), (4850.241033380682, 5186.058549360796)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_38.npy'}) Paths in Results Directory: ../results/segmentation_result_38.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/tile_16/run_spec.pkl ../data/merscope_run/experiment.json ../data/merscope_run/polyt.png ../data/merscope_run/dapi.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((904.7367458343506, 1231.8456732432048), (4238.606001420454, 4574.423517400568)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_16.npy'}) Paths in Results Directory: ../results/segmentation_result_16.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/tile_22/run_spec.pkl ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((2687.3903102874756, 3014.4992376963296), (4238.606001420454, 4574.423517400568)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_22.npy'}) Paths in Results Directory: ../results/segmentation_result_22.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/tile_36/run_spec.pkl ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((1796.063528060913, 2123.172455469767), (4850.241033380682, 5186.058549360796)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_36.npy'}) Paths in Results Directory: ../results/segmentation_result_36.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/tile_29/run_spec.pkl Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((2390.2813828786216, 2717.3903102874756), (4544.423517400568, 4880.241033380682)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_29.npy'}) Paths in Results Directory: ../results/segmentation_result_29.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/tile_20/run_spec.pkl Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((2093.1724554697676, 2420.2813828786216), (4238.606001420454, 4574.423517400568)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_20.npy'}) Paths in Results Directory: ../results/segmentation_result_20.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/tile_30/run_spec.pkl ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((2687.3903102874756, 3014.4992376963296), (4544.423517400568, 4880.241033380682)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_30.npy'}) Paths in Results Directory: ../results/segmentation_result_30.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev ../data/tile_35/run_spec.pkl ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((1498.954600652059, 1826.0635280609133), (4850.241033380682, 5186.058549360796)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_35.npy'}) Paths in Results Directory: ../results/segmentation_result_35.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/tile_37/run_spec.pkl ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((2093.1724554697676, 2420.2813828786216), (4850.241033380682, 5186.058549360796)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_37.npy'}) Paths in Results Directory: ../results/segmentation_result_37.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/tile_26/run_spec.pkl Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((1201.8456732432048, 1528.954600652059), (4544.423517400568, 4880.241033380682)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_26.npy'}) Paths in Results Directory: ../results/segmentation_result_26.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/tile_28/run_spec.pkl ../data/merscope_run/experiment.json ../data/merscope_run/polyt.png ../data/merscope_run/dapi.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((1796.063528060913, 2123.172455469767), (4544.423517400568, 4880.241033380682)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_28.npy'}) Paths in Results Directory: ../results/segmentation_result_28.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/tile_27/run_spec.pkl ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((1498.954600652059, 1826.0635280609133), (4544.423517400568, 4880.241033380682)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_27.npy'}) Paths in Results Directory: ../results/segmentation_result_27.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/tile_3/run_spec.pkl ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((1201.8456732432048, 1528.954600652059), (3626.970969460227, 3962.7884854403405)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_3.npy'}) Paths in Results Directory: ../results/segmentation_result_3.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/tile_18/run_spec.pkl ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev ../data/merscope_run/experiment.json ../data/merscope_run/polyt.png ../data/merscope_run/dapi.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((1498.954600652059, 1826.0635280609133), (4238.606001420454, 4574.423517400568)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_18.npy'}) Paths in Results Directory: ../results/segmentation_result_18.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/tile_39/run_spec.pkl ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((2687.3903102874756, 3014.4992376963296), (4850.241033380682, 5186.058549360796)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_39.npy'}) Paths in Results Directory: ../results/segmentation_result_39.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/tile_23/run_spec.pkl ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((310.51889101664227, 637.6278184254965), (4544.423517400568, 4880.241033380682)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_23.npy'}) Paths in Results Directory: ../results/segmentation_result_23.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/tile_44/run_spec.pkl ../data/cellpose_model/CP_20240611_mousedev ../data/cellpose_model/._CP_20240612_mousedev ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((1796.063528060913, 2123.172455469767), (5156.058549360796, 5491.87606534091)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_44.npy'}) Paths in Results Directory: ../results/segmentation_result_44.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev ../data/tile_34/run_spec.pkl Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((1201.8456732432048, 1528.954600652059), (4850.241033380682, 5186.058549360796)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_34.npy'}) Paths in Results Directory: ../results/segmentation_result_34.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev ../data/tile_31/run_spec.pkl Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((310.51889101664227, 637.6278184254965), (4850.241033380682, 5186.058549360796)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_31.npy'}) Paths in Results Directory: ../results/segmentation_result_31.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/tile_43/run_spec.pkl Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((1201.8456732432048, 1528.954600652059), (5156.058549360796, 5491.87606534091)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_43.npy'}) Paths in Results Directory: ../results/segmentation_result_43.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/tile_45/run_spec.pkl ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((607.6278184254965, 934.7367458343506), (5461.876065340909, 5797.693581321023)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_45.npy'}) Paths in Results Directory: ../results/segmentation_result_45.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/merscope_run/experiment.json ../data/merscope_run/polyt.png ../data/merscope_run/dapi.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/tile_49/run_spec.pkl ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((607.6278184254965, 934.7367458343506), (5767.693581321022, 6103.511097301136)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_49.npy'}) Paths in Results Directory: ../results/segmentation_result_49.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/tile_40/run_spec.pkl ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((310.51889101664227, 637.6278184254965), (5156.058549360796, 5491.87606534091)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_40.npy'}) Paths in Results Directory: ../results/segmentation_result_40.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev ../data/tile_24/run_spec.pkl ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((607.6278184254965, 934.7367458343506), (4544.423517400568, 4880.241033380682)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_24.npy'}) Paths in Results Directory: ../results/segmentation_result_24.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev ../data/tile_25/run_spec.pkl ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((904.7367458343506, 1231.8456732432048), (4544.423517400568, 4880.241033380682)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_25.npy'}) Paths in Results Directory: ../results/segmentation_result_25.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev ../data/tile_50/run_spec.pkl ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((904.7367458343506, 1231.8456732432048), (5767.693581321022, 6103.511097301136)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_50.npy'}) Paths in Results Directory: ../results/segmentation_result_50.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev ../data/tile_46/run_spec.pkl ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((904.7367458343506, 1231.8456732432048), (5461.876065340909, 5797.693581321023)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_46.npy'}) Paths in Results Directory: ../results/segmentation_result_46.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/tile_19/run_spec.pkl ../data/merscope_run/experiment.json ../data/merscope_run/polyt.png ../data/merscope_run/dapi.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((1796.063528060913, 2123.172455469767), (4238.606001420454, 4574.423517400568)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_19.npy'}) Paths in Results Directory: ../results/segmentation_result_19.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/tile_7/run_spec.pkl ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((607.6278184254965, 934.7367458343506), (3932.788485440341, 4268.606001420455)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_7.npy'}) Paths in Results Directory: ../results/segmentation_result_7.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/tile_47/run_spec.pkl ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((1498.954600652059, 1826.0635280609133), (5461.876065340909, 5797.693581321023)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_47.npy'}) Paths in Results Directory: ../results/segmentation_result_47.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/tile_51/run_spec.pkl Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((1201.8456732432048, 1528.954600652059), (5767.693581321022, 6103.511097301136)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_51.npy'}) Paths in Results Directory: ../results/segmentation_result_51.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/tile_33/run_spec.pkl ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((904.7367458343506, 1231.8456732432048), (4850.241033380682, 5186.058549360796)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_33.npy'}) Paths in Results Directory: ../results/segmentation_result_33.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev ../data/tile_48/run_spec.pkl Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((1796.063528060913, 2123.172455469767), (5461.876065340909, 5797.693581321023)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_48.npy'}) Paths in Results Directory: ../results/segmentation_result_48.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/merscope_run/experiment.json ../data/merscope_run/polyt.png ../data/merscope_run/dapi.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/tile_52/run_spec.pkl ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((1498.954600652059, 1826.0635280609133), (5767.693581321022, 6103.511097301136)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_52.npy'}) Paths in Results Directory: ../results/segmentation_result_52.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/merscope_run/experiment.json ../data/merscope_run/polyt.png ../data/merscope_run/dapi.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/tile_32/run_spec.pkl ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((607.6278184254965, 934.7367458343506), (4850.241033380682, 5186.058549360796)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_32.npy'}) Paths in Results Directory: ../results/segmentation_result_32.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev ../data/tile_4/run_spec.pkl ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((1498.954600652059, 1826.0635280609133), (3626.970969460227, 3962.7884854403405)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_4.npy'}) Paths in Results Directory: ../results/segmentation_result_4.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev ../data/tile_17/run_spec.pkl Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((1201.8456732432048, 1528.954600652059), (4238.606001420454, 4574.423517400568)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_17.npy'}) Paths in Results Directory: ../results/segmentation_result_17.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/merscope_run/experiment.json ../data/merscope_run/polyt.png ../data/merscope_run/dapi.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/tile_42/run_spec.pkl ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((904.7367458343506, 1231.8456732432048), (5156.058549360796, 5491.87606534091)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_42.npy'}) Paths in Results Directory: ../results/segmentation_result_42.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/tile_6/run_spec.pkl Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((2093.1724554697676, 2420.2813828786216), (3626.970969460227, 3962.7884854403405)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_6.npy'}) Paths in Results Directory: ../results/segmentation_result_6.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev ../data/tile_41/run_spec.pkl ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((607.6278184254965, 934.7367458343506), (5156.058549360796, 5491.87606534091)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_41.npy'}) Paths in Results Directory: ../results/segmentation_result_41.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/tile_8/run_spec.pkl ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev ../data/merscope_run/experiment.json ../data/merscope_run/polyt.png ../data/merscope_run/dapi.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((904.7367458343506, 1231.8456732432048), (3932.788485440341, 4268.606001420455)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_8.npy'}) Paths in Results Directory: ../results/segmentation_result_8.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/tile_5/run_spec.pkl ../data/merscope_run/experiment.json ../data/merscope_run/polyt.png ../data/merscope_run/dapi.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((1796.063528060913, 2123.172455469767), (3626.970969460227, 3962.7884854403405)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_5.npy'}) Paths in Results Directory: ../results/segmentation_result_5.npy [capsule-8021045] completed! [capsule-8021045] cloning git repo... [capsule-8021045] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/tile_9/run_spec.pkl ../data/cellpose_model/._CP_20240612_mousedev ../data/cellpose_model/CP_20240611_mousedev ../data/merscope_run/experiment.json ../data/merscope_run/polyt.png ../data/merscope_run/dapi.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': ((1201.8456732432048, 1528.954600652059), (3932.788485440341, 4268.606001420455)), 'method_class': , 'method_args': {'options': {'cellpose_model': '../data/cellpose_model/CP_20240611_mousedev', 'cellpose_gpu': 'auto', 'px_size': 0.108, 'cell_dia': 10.0, 'z_plane_thickness': 1.5, 'images': {'cyto': {'channel': 'total_mrna', 'n_planes': 7}, 'nuclei': {'channel': 'DAPI'}}, 'cellpose_options': {'batch_size': 8, 'min_size': 5000}}}, 'result_file': None, 'cell_id_file': '../results/segmentation_result_9.npy'}) Paths in Results Directory: ../results/segmentation_result_9.npy [capsule-8021045] completed! [52/266da3] Submitted process > capsule_merge_segmented_tiles_3 (capsule-9631821) [capsule-9631821] cloning git repo... [capsule-9631821] running capsule... Paths in Data Directory: ../data/SegmentationPipeline.pkl ../data/seg_tiles/segmentation_result_48.npy ../data/seg_tiles/segmentation_result_13.npy ../data/seg_tiles/segmentation_result_33.npy ../data/seg_tiles/segmentation_result_0.npy ../data/seg_tiles/segmentation_result_52.npy ../data/seg_tiles/segmentation_result_1.npy ../data/seg_tiles/segmentation_result_32.npy ../data/seg_tiles/segmentation_result_12.npy ../data/seg_tiles/segmentation_result_41.npy ../data/seg_tiles/segmentation_result_14.npy ../data/seg_tiles/segmentation_result_8.npy ../data/seg_tiles/segmentation_result_11.npy ../data/seg_tiles/segmentation_result_5.npy ../data/seg_tiles/segmentation_result_15.npy ../data/seg_tiles/segmentation_result_9.npy ../data/seg_tiles/segmentation_result_2.npy ../data/seg_tiles/segmentation_result_21.npy ../data/seg_tiles/segmentation_result_16.npy ../data/seg_tiles/segmentation_result_10.npy ../data/seg_tiles/segmentation_result_38.npy ../data/seg_tiles/segmentation_result_36.npy ../data/seg_tiles/segmentation_result_22.npy ../data/seg_tiles/segmentation_result_29.npy ../data/seg_tiles/segmentation_result_20.npy ../data/seg_tiles/segmentation_result_35.npy ../data/seg_tiles/segmentation_result_37.npy ../data/seg_tiles/segmentation_result_30.npy ../data/seg_tiles/segmentation_result_26.npy ../data/seg_tiles/segmentation_result_27.npy ../data/seg_tiles/segmentation_result_28.npy ../data/seg_tiles/segmentation_result_3.npy ../data/seg_tiles/segmentation_result_18.npy ../data/seg_tiles/segmentation_result_39.npy ../data/seg_tiles/segmentation_result_44.npy ../data/seg_tiles/segmentation_result_23.npy ../data/seg_tiles/segmentation_result_34.npy ../data/seg_tiles/segmentation_result_31.npy ../data/seg_tiles/segmentation_result_43.npy ../data/seg_tiles/segmentation_result_45.npy ../data/seg_tiles/segmentation_result_49.npy ../data/seg_tiles/segmentation_result_24.npy ../data/seg_tiles/segmentation_result_40.npy ../data/seg_tiles/segmentation_result_25.npy ../data/seg_tiles/segmentation_result_50.npy ../data/seg_tiles/segmentation_result_46.npy ../data/seg_tiles/segmentation_result_19.npy ../data/seg_tiles/segmentation_result_7.npy ../data/seg_tiles/segmentation_result_47.npy ../data/seg_tiles/segmentation_result_51.npy ../data/seg_tiles/segmentation_result_4.npy ../data/seg_tiles/segmentation_result_17.npy ../data/seg_tiles/segmentation_result_42.npy ../data/seg_tiles/segmentation_result_6.npy ../data/seg_tiles/tile_1/run_spec.pkl ../data/seg_tiles/tile_43/run_spec.pkl ../data/seg_tiles/tile_11/run_spec.pkl ../data/seg_tiles/tile_45/run_spec.pkl ../data/seg_tiles/tile_12/run_spec.pkl ../data/seg_tiles/tile_46/run_spec.pkl ../data/seg_tiles/tile_14/run_spec.pkl ../data/seg_tiles/tile_47/run_spec.pkl ../data/seg_tiles/tile_13/run_spec.pkl ../data/seg_tiles/tile_48/run_spec.pkl ../data/seg_tiles/tile_15/run_spec.pkl ../data/seg_tiles/tile_49/run_spec.pkl ../data/seg_tiles/tile_16/run_spec.pkl ../data/seg_tiles/tile_5/run_spec.pkl ../data/seg_tiles/tile_17/run_spec.pkl ../data/seg_tiles/tile_50/run_spec.pkl ../data/seg_tiles/tile_18/run_spec.pkl ../data/seg_tiles/tile_51/run_spec.pkl ../data/seg_tiles/tile_19/run_spec.pkl ../data/seg_tiles/tile_52/run_spec.pkl ../data/seg_tiles/tile_2/run_spec.pkl ../data/seg_tiles/tile_6/run_spec.pkl ../data/seg_tiles/tile_20/run_spec.pkl ../data/seg_tiles/tile_7/run_spec.pkl ../data/seg_tiles/tile_22/run_spec.pkl ../data/seg_tiles/tile_8/run_spec.pkl ../data/seg_tiles/tile_21/run_spec.pkl ../data/seg_tiles/tile_9/run_spec.pkl ../data/seg_tiles/tile_23/run_spec.pkl ../data/seg_tiles/tile_24/run_spec.pkl ../data/seg_tiles/tile_25/run_spec.pkl ../data/seg_tiles/tile_26/run_spec.pkl ../data/seg_tiles/tile_27/run_spec.pkl ../data/seg_tiles/tile_28/run_spec.pkl ../data/seg_tiles/tile_3/run_spec.pkl ../data/seg_tiles/tile_29/run_spec.pkl ../data/seg_tiles/tile_30/run_spec.pkl ../data/seg_tiles/tile_32/run_spec.pkl ../data/seg_tiles/tile_33/run_spec.pkl ../data/seg_tiles/tile_31/run_spec.pkl ../data/seg_tiles/tile_34/run_spec.pkl ../data/seg_tiles/tile_35/run_spec.pkl ../data/seg_tiles/tile_36/run_spec.pkl ../data/seg_tiles/tile_37/run_spec.pkl ../data/seg_tiles/tile_38/run_spec.pkl ../data/seg_tiles/tile_39/run_spec.pkl ../data/seg_tiles/tile_4/run_spec.pkl ../data/seg_tiles/tile_40/run_spec.pkl ../data/seg_tiles/tile_41/run_spec.pkl ../data/seg_tiles/tile_42/run_spec.pkl ../data/seg_tiles/tile_0/run_spec.pkl ../data/seg_tiles/tile_10/run_spec.pkl ../data/seg_tiles/tile_44/run_spec.pkl len(seg_pipeline.raw_spot_table)=16398139 Pre-Merge: len(seg_spot_table)=16398139 Pre-Merge: len(seg_spot_table.cell_ids)=16398139 Post-Merge: len(seg_spot_table)=16398139 Post-Merge: len(seg_spot_table.cell_ids)=16398139 Paths in Results Directory: ../results/segmentation.npy ../results/seg_spot_table.npz ../results/example_plot.png [capsule-9631821] completed! [c1/be65c7] Submitted process > capsule_splitpolygons_4 (capsule-2807919) [capsule-2807919] cloning git repo... [capsule-2807919] running capsule... Paths in Data Directory: ../data/example_plot.png ../data/segmentation.npy ../data/seg_spot_table.npz ../data/SegmentationPipeline.pkl Arguments: --num-jobs 0 --cells-per-job 10000 --alpha-inv-coeff 4/3 len(seg_spot_table)=16398139 Number of Cells=22145 Number of Polygon Jobs=3 Evaluated alpha_inv_coeff=1.33333 Paths in Results Directory: ../results/job_0/cell_id_subset.npy ../results/job_0/run_spec.pkl ../results/job_0/segmentation.npy ../results/job_1/cell_id_subset.npy ../results/job_1/run_spec.pkl ../results/job_1/segmentation.npy ../results/job_2/cell_id_subset.npy ../results/job_2/run_spec.pkl ../results/job_2/segmentation.npy [capsule-2807919] completed! [64/c7f6b0] Submitted process > capsule_polygon_run_5 (capsule-4008213) [bb/057568] Submitted process > capsule_polygon_run_5 (capsule-4008213) [31/c58756] Submitted process > capsule_polygon_run_5 (capsule-4008213) [capsule-4008213] cloning git repo... [capsule-4008213] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/job_2/cell_id_subset.npy ../data/job_2/run_spec.pkl ../data/job_2/segmentation.npy Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': 'DAPI', 'cell_id_file': '../data/job_2/segmentation.npy', 'cell_subset_file': '../data/job_2/cell_id_subset.npy', 'result_file': '../results/cell_polygons_subset_2.geojson', 'alpha_inv_coeff': 1.3333333333333333}) Paths in Results Directory: ../results/cell_polygons_subset_2.geojson [capsule-4008213] completed! [capsule-4008213] cloning git repo... [capsule-4008213] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/job_0/cell_id_subset.npy ../data/job_0/run_spec.pkl ../data/job_0/segmentation.npy Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': 'DAPI', 'cell_id_file': '../data/job_0/segmentation.npy', 'cell_subset_file': '../data/job_0/cell_id_subset.npy', 'result_file': '../results/cell_polygons_subset_0.geojson', 'alpha_inv_coeff': 1.3333333333333333}) Paths in Results Directory: ../results/cell_polygons_subset_0.geojson [capsule-4008213] completed! [capsule-4008213] cloning git repo... [capsule-4008213] running capsule... Paths in Data Directory: ../data/detected_transcripts.csv.npz ../data/merscope_run/experiment.json ../data/merscope_run/dapi.png ../data/merscope_run/polyt.png ../data/merscope_run/region_0/cell_metadata.csv ../data/merscope_run/region_0/cell_by_gene.csv ../data/merscope_run/region_0/cell_boundaries.parquet ../data/merscope_run/region_0/202403010955_1326981592_VMSC05501_region_0.vzg ../data/merscope_run/region_0/detected_transcripts.csv ../data/merscope_run/region_0/summary.png ../data/merscope_run/region_0/images/manifest.json ../data/merscope_run/region_0/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_0/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_0/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_0/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_1/cell_boundaries.parquet ../data/merscope_run/region_1/cell_metadata.csv ../data/merscope_run/region_1/cell_by_gene.csv ../data/merscope_run/region_1/202403010955_1326981592_VMSC05501_region_1.vzg ../data/merscope_run/region_1/detected_transcripts.csv ../data/merscope_run/region_1/summary.png ../data/merscope_run/region_1/images/manifest.json ../data/merscope_run/region_1/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_1/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_1/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_1/images/mosaic_PolyT_z6.tif ../data/merscope_run/region_2/cell_boundaries.parquet ../data/merscope_run/region_2/cell_by_gene.csv ../data/merscope_run/region_2/cell_metadata.csv ../data/merscope_run/region_2/202403010955_1326981592_VMSC05501_region_2.vzg ../data/merscope_run/region_2/detected_transcripts.csv ../data/merscope_run/region_2/summary.png ../data/merscope_run/region_2/images/manifest.json ../data/merscope_run/region_2/images/micron_to_mosaic_pixel_transform.csv ../data/merscope_run/region_2/images/mosaic_DAPI_z1.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z0.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z2.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z3.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z4.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z5.tif ../data/merscope_run/region_2/images/mosaic_DAPI_z6.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z0.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z1.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z2.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z3.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z4.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z5.tif ../data/merscope_run/region_2/images/mosaic_PolyT_z6.tif ../data/job_1/run_spec.pkl ../data/job_1/cell_id_subset.npy ../data/job_1/segmentation.npy Run Spec: (, (), {'load_func': >, 'load_args': {'image_path': '../data/merscope_run/region_0/images', 'csv_file': '../data/merscope_run/region_0/detected_transcripts.csv', 'cache_file': '../data/detected_transcripts.csv.npz', 'max_rows': None}, 'subregion': 'DAPI', 'cell_id_file': '../data/job_1/segmentation.npy', 'cell_subset_file': '../data/job_1/cell_id_subset.npy', 'result_file': '../results/cell_polygons_subset_1.geojson', 'alpha_inv_coeff': 1.3333333333333333}) Paths in Results Directory: ../results/cell_polygons_subset_1.geojson [capsule-4008213] completed! [78/4b315f] Submitted process > capsule_polygon_merge_6 (capsule-8779472) [capsule-8779472] cloning git repo... [capsule-8779472] running capsule... Paths in Data Directory: ../data/cell_polygons_subset_2.geojson ../data/cell_polygons_subset_1.geojson ../data/cell_polygons_subset_0.geojson ../data/seg_spot_table.npz len(seg_spot_table)=16398139 len(seg_spot_table.cell_polygons)=22145 Paths in Results Directory: ../results/cell_polygons.geojson ../results/seg_spot_table.npz [capsule-8779472] completed! [23/f5f590] Submitted process > capsule_create_cell_by_genetable_7 (capsule-9688787) [capsule-9688787] cloning git repo... [capsule-9688787] running capsule... Paths in Data Directory: ../data/seg_spot_table.npz Arguments: --anndata-X-format sparse --cell-id-prefix 1326981611_CP --cell-id-suffix None len(seg_spot_table)=16398139 Number of Cells (SST)=22145 Number of Cells (AnnData)=22145 Paths in Results Directory: ../results/cell_by_gene.h5ad ../results/segmented_spot_table.csv [capsule-9688787] completed! Waiting for file transfers to complete (1 files)