This repository contains 140 gene MERFISH spatial transcriptomics data collected from mouse retina (n=8 samples) from Nimkar et al. 2025.

Each folder 140g_rn[x] is 1 mouse, consisting of several separately imaged tissue sections (140g_rn[x]_rg[y]).

For each tissue section, there is a "raw" folder containing Vizgen boundary stain images (Cellbound2), and some of them also contain CD31 (Anti-Rat channel) or contain Opn4 (Cellbound3) staining. There are also "procesed folders containing the stitched segmentation masks. If a given raw image zstack is of shape (y,x), the stitched masks are of shape (z,y//4,x//4) as the images are resized presegmentation and the final stitched_masks includes all the zstacks merged togther. Finally, there is a "transcripts" folder that contains the Vizgen provided transcripts as well as a matrix that transforms the transcript coordinate system to the original raw pixel coordinate system.