This data collection contains spatially resolved single-cell transcriptomics datasets acquired using MERFISH applied to olfactory receptor genes on the mouse main olfactory bulb (MOB) collected by the Catherine Dulac and Xiaowei Zhuang Labs at Harvard University and Howard Hughes Medical Institute.

* The dataset contains MERFISH images of serial coronal sections of the MOB region (16 um thick slices) across 2 female animals. The MOB of each animal was harvested and cryosectioned across 140-200 serial coronal slices per animal covering approximately the entire olfactory bulbs (covering both the left and right hemispheres) across 2 biological replicates. The serial slices are numbered in order in the posterior to anterior direction. We note that some slice numbers are missing indicating that the corresponding serial section was not successfully imaged either due to a failure in the sample preparation or during imaging. For each slice one of two orthogonal sets of olfactory receptor genes (gene_set1 or  gene_set2 - each with 500-600 genes) was imaged in an approximately alternating manner across sections. Bellow is a list of the indices of slices of the 2 animals that were imaged with gene_set1 or gene_set2:
Indexes of mouse1 slices using gene_set1: 1, 2, 5, 6, 9, 10, 13, 14, 17, 18, 21, 22, 25, 26, 29, 30, 33, 34, 37, 38, 41, 42, 45, 46, 49, 50, 53, 54, 57, 58, 61, 62, 65, 66, 69, 70, 73, 74, 77, 78, 81, 82, 86, 89, 90, 93, 94, 98, 102, 110, 114, 118, 122, 126, 130, 134, 138, 142, 145, 146, 149, 150, 153, 154, 157, 158, 161, 162, 165, 166

Indexes of mouse1 slices using gene_set2: 3, 4, 7, 8, 11, 12, 15, 16, 19, 20, 23, 24, 27, 28, 31, 32, 35, 36, 39, 40, 43, 44, 47, 48, 51, 52, 55, 56, 59, 60, 63, 64, 67, 68, 71, 72, 75, 76, 79, 80, 83, 84, 87, 88, 92, 96, 99, 100, 104, 107, 111, 112, 115, 116, 119, 121, 123, 125, 127, 129, 131, 133, 137, 139, 141, 143, 147, 151, 155, 159, 163, 167

Indexes of mouse2 slices using gene_set1: 1, 2, 5, 6, 9, 10, 12, 13, 16, 17, 20, 21, 24, 25, 28, 29, 32, 33, 36, 37, 40, 41, 44, 45, 49, 50, 53, 54, 57, 58, 61, 62, 65, 66, 69, 70, 73, 74, 77, 78, 81, 82, 85, 86, 89, 90, 93, 94, 97, 98, 99, 101, 102, 103, 105, 106, 107, 109, 110, 111, 113, 114, 115, 117, 118, 119, 123, 127, 131, 135, 139, 143, 144, 147, 148, 151, 152, 155, 156, 159, 160, 163, 166, 167, 170, 171, 174, 175, 178, 179, 182, 183, 186, 187, 190, 191, 194, 195, 198, 199, 202, 203, 205, 206, 207, 211, 212

Indexes of mouse2 slices using gene_set2: 3, 4, 7, 8, 11, 14, 15, 18, 19, 22, 23, 26, 27, 30, 31, 34, 35, 38, 39, 42, 43, 46, 47, 48, 51, 52, 55, 56, 59, 60, 63, 64, 67, 68, 71, 72, 75, 76, 79, 80, 83, 84, 87, 88, 91, 92, 95, 96, 100, 104, 108, 112, 116, 120, 121, 122, 124, 125, 126, 128, 129, 130, 132, 133, 134, 136, 137, 138, 140, 141, 142, 145, 146, 149, 150, 153, 154, 157, 158, 161, 162, 164, 165, 168, 169, 172, 173, 176, 177, 180, 181, 184, 185, 188, 189, 192, 193, 196, 197, 200, 201, 204, 208, 209, 210, 213


* In this dataset, a total of ~1100 olfactory receptor genes were imaged using MERFISH. MERFISH encodes individual genes with error-robust barcodes (15-bit binary codes in this case), imprints the barcodes onto the RNAs using combinatorial labeling with encoding probes, and measures the barcodes bit-by-bit using sequential hybridization of readout probes. The 15 bits are imaged in 5 hybridization rounds with 3-color imaging each round. 
* There are two subdirectory folders: mouse1 and mouse2 corresponding to the two biological replicates. Each of these directories contains 140-210 subdirectories labelled Slice_{index} each containing the raw images of one coronal slice in the series. Each slice is covered by many fields of view (FOVs) and each tiff file in the folder corresponds to the images of one FOV. The raw image files are named as "ims_" plus the FOV id (e.g. ims_0001.tif). Each raw image file, corresponding to one FOV, is a stacked tiff file of multiple frames, each frame corresponding to one z-plane of one channel and each channel corresponding to one bit of the MERFISH imaging process, or the nuclear signal, restrained using DAPI, after each round of hybridization. The tiff stacks are ordered, for example, as channel 1 z-planes 1 through 50, channel 2 z-planes 1 through 50, ... , channel 20 z-plane 1 through 50. The last 5 channels, corresponding to the nuclear signal reimaged after each round of hybridization, are used to align the first 15 readout channels (3 readout channels per round). See data_organization.csv file in the additiona_files folder for detailed channel information for each experiment.
* Upon determining via MERFISH the number of molecules corresponding to each olfactory receptor in each segmented glomeruli, we use the following QC criteria to determine the identity of glomeruli: 
1) First, within the segmented area of each glomeruli in each olfactory bulb slice, we determine the number of RNA molecules of the most abundant receptor gene. If this number is above 10 molecules and it is at least 10 times higher than the average number of transcripts of the corresponding receptor in the surrounding 50 glomeruli, then we assign the identity of the glomeruli to this, most abundant, receptor. Otherwise, we do not assign an identity to this glomeruli.
2) If the positions of the glomeruli with the same most abundant receptor are less than 500 um across multiple aligned olfactory bulbs, then we reduce the above abundance and specificity cutoffs to: above 7 molecules and at least 7.5 times higher expression than the surrounding glomeruli.
We considered a dataset of acceptable quality if by using the criteria described above we determine the projections of at least 40% of the olfactory receptor gene repertoire. This takes into account both the quality of transcripts remaining upon the molecular biology treatments of the sample, the quality of the MERFISH imaging and the quality of the dissection/sectioning of the olfactory bulbs.


* The processed_data folder contains the following file:
- segmented_glomeruli.csv: Across all the slices of the 2 replicates we provide the boundaries of each segmented glomeruli whose olfactory receptor identity we have determined upon passing the QC criteria. The boundaries are provided in um, relative to the corner of the corresponding field of view. When glomeruli are covered by multiple fields of view, multiple sets of boundaries are provided, ordered by the index of the field of view. We also provide absolute positions, in um, of the center of each identified glomeruli in a coordinate system in which the four total olfactory bulbs (the left and the right bulb of each animal) have been aligned to a single reference. We provide information for each glomeruli of the corresponding animal as "mouse_id", the slice index as "slice_id", the fields of view as "fov_id" and the corresponding left or right hemisphere using the 1 or 0 respectively for "left_right_id" . We note that each MERFISH experiment includes 4-6 tissue slices on a single coverslip, and we mark for each glomeruli the experimental index under "experiment_id". As the last two entries, we provide for each glomeruli two QC measures: the number of the corresponding olfactory receptor's RNA molecules and a specificity score indicating how much more the receptor transcripts are enriched in the volume of the current glomeruli over the surrounding glomeruli.

We also provide these files that are associated to this dataset:
*	probes.fasta: Contains the sequences of all encoding probes used for hybridization in this dataset.
*	codebook.csv: Provides the barcodes that encode individual genes measured in the combinatorial imaging rounds. We note that a single barcoding scheme was constructed for all ~1100 olfactory genes. While this enables imaging of all of the olfactory receptor genes in a single experiment, for better decoding performance we selected to image 500-600 olfactory genes per experiment.
*	genes_set1/2.txt: List of the olfactory receptor genes corresponding to the two sets of 500/600 receptor genes imaged per experiment.
*	data_organization.csv: Provides information on how individual channels and z-planes are ordered in the multi-frame tiff file of each field of view of the raw images.
*    fov_positions.csv: Provides tabulated information of the x and y postions (in um) of the center of each field of view ("fov_id") of each slice ("slice_id") in each animal ("mouse_id").
*	microscope.json: Provides parameters of the microscope that was used for each experiment with pixel size and orientation of images.