Ultrasensitive, sequential flourescence in situ hybridization (USeqFISH) is a highly sensitive spatial transcriptomics method for profiling endogenous and virally-delivered genes in intact mouse and non-human primates.
This is data analysis pipeline for images generated in USeqFISH.
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To get a local copy up and running follow these simple example steps.
- Clone the repo
git clone https://github.com/minjeejang/useqfish_analysis.git
- Install Requirements
pip install --upgrade pip pip install -r requirements.txt
To run the pipeline, you'll need multiple round images in .tif format.
Open params.py and set the parameters for your project.
- nC: Number of channels each round has
- nR: Number of total rounds
- roundRef: Which round contains the cell reference
- cellCh: channel containing cell reference
- image_size: image size in pixels
- sigma: estimate size of spots to detect
- color_shifts: channel shifts for each channel, provided by the equipment
python get_expression_matrix.py [path][path] is the path to the directory containting your images. All .tif images in this path will be analyzed. Note: script will take a while (30 minutes+) to run, depending on image size and machine specifications.
Once the run is finished, there will be a results.xlsx file in your image path. This contains a the expression by cell ID.