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

* The dataset contains MERFISH images of coronal sections of the MOE region (16 um thick slices) across animals of different gender exposed to different odors (female mouse odor, male mouse odor and cat odor). The animals were single-housed in a cage for ~1 week after which an intruder animal or cat bedding was introduced into the cage. After 30 minutes of free interaction, the host animal was sacrificed and its MOE harvested. 10-14 coronal slices of the MOE region were collected from 2 biological replicates for each condition. For each mouse, 2-3 experiments were performed using different sets of genes (see details in the section below), and each experiment was named with the mouse id plus the sample id.

mouse1_sample1 - corresponds to a male mouse (replicate 1)exposed  to female odor and imaging the first olfactory gene set.
mouse1_sample2 - corresponds to a male mouse (replicate 1)exposed  to female odor and imaging the second olfactory gene set.
mouse2_sample1 - corresponds to a male mouse (replicate 2)exposed  to female odor and imaging the first olfactory gene set.
mouse2_sample2 - corresponds to a male mouse (replicate 2)exposed  to female odor and imaging the second olfactory gene set.
mouse3_sample1 - corresponds to a female mouse (replicate 1)exposed  to male odor and imaging the first olfactory gene set.
mouse3_sample2 - corresponds to a female mouse (replicate 1)exposed  to male odor and imaging the second olfactory gene set.
mouse4_sample1 - corresponds to a female mouse (replicate 2)exposed  to male odor and imaging the first olfactory gene set.
mouse4_sample2 - corresponds to a female mouse (replicate 2)exposed  to male odor and imaging the second olfactory gene set.
mouse4_sample3 - corresponds to a female mouse (replicate 2)exposed  to male odor and imaging the third olfactory gene set.
mouse5_sample1 - corresponds to a male mouse (replicate 1)exposed  to cat odor and imaging the first olfactory gene set.
mouse5_sample2 - corresponds to a male mouse (replicate 1)exposed  to cat odor and imaging the second olfactory gene set.
mouse6_sample1 - corresponds to a male mouse (replicate 2)exposed  to cat odor and imaging the first olfactory gene set.
mouse6_sample2 - corresponds to a male mouse (replicate 2)exposed  to cat odor and imaging the second olfactory gene set.
mouse7_sample1 - corresponds to a male mouse (replicate 1)exposed  to male odor and imaging the first olfactory gene set.
mouse7_sample2 - corresponds to a male mouse (replicate 1)exposed  to male odor and imaging the second olfactory gene set.
mouse8_sample1 - corresponds to a male mouse (replicate 2)exposed  to male odor and imaging the first olfactory gene set.
mouse8_sample2 - corresponds to a male mouse (replicate 2)exposed  to male odor or and imaging the second olfactory gene set.
mouse9_sample1 - corresponds to a female mouse (replicate 1)exposed  to female odor and imaging the first olfactory gene set.
mouse9_sample2 - corresponds to a female mouse (replicate 1)exposed  to female odor and imaging the second olfactory gene set.
mouse10_sample1 - corresponds to a female mouse (replicate 2)exposed  to female odor and imaging the first olfactory gene set.
mouse10_sample2 - corresponds to a male mouse (replicate 2)exposed  to female odor and imaging the second olfactory gene set.

For each experiment, multiple coronal slices (3-7 slices) were included on the same coverslip and were imaged together.

* In this dataset, a total of ~1100  genes were imaged. Among these 1 gene (EGR1), marking the activity of the sensory neurons, was imaged first in a single color channel. The EGR1 signal was then quenched and hundreds of 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 8 or 5 hybridization rounds with 3-color or 2-color imaging each round. 
* Each of the subdirectory {mouse_id_sample_id} folders (e.g. mouse1_sample1) contains the raw images of one experiment. Each experiment contains 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 aligned_images plus the FOV id (e.g. aligned_images0.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 EGR1 activity signal, or the nuclear signal (stained with DAPI). Images are aligned using the nuclear signal reimaged across each imaging round. The tiff stacks are ordered, for example, as channel 1 z-planes 1 through 50, channel 2 z-planes 1 through 50, ... , channel 17 z-plane 1 through 50. See data_organization_{mouse_id_sample_id}.csv file in the additiona_files folder for detailed channel information for each experiment.


* The processed_data folder contains the following files:
- segmented_cells_{mouse_id_sample_id}.csv: For each experiment we provide the boundaries of each segmented olfactory receptor cell in um, relative to the corner of the corresponding field of view. We also provide absolute positions, in um, of the center of each cell in coordinates relative to the stage and the slice and field of view id that each cell belongs to. Note that each experiment includes 3-7 tissue slices on a single coverslip, and the slice id gives the slice number that the cells belong to. As the last entry, we provide for each cell the number of RNA molecules of the activity marker EGR1 for each exposure condition mentioned.

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 all of the olfactory receptor genes in a single experiment, for better decoding performance we selected to image 300-600 olfactory genes per experiment.
*	genes_{mouse_id_sample_id}.txt: List of the olfactory receptor genes that are imaged in each experiment {mouse_id_sample_id}.
*	data_organization_{mouse_id_sample_id}.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.
*	microscope_{mouse_id_sample_id}.json: Provides parameters of the microscope that was used for each experiment with pixel size and orientation of images.