This repository contains the notebooks used for the 2023 I2K workshop on spatial transcriptomics data analysis.
The data used in this worksop was published along the paper Cell segmentation in imaging-based spatial transcriptomics.
Download the data from here and unzip it inside this folder.
Citation:
Moffitt, Jeffrey et al. (2021). MERFISH measurements in the mouse ileum [Dataset]. Dryad
Create a new conda environment containing the required python packages:
conda env create -f environment.yml
Activate the environment to run the notebooks:
conda activate <env-name>
The repository contains two notebooks:
baysor_output.ipynb provides code to read and inspec the raw data.
merfish_analysis.ipynb provides code fro a simple analysis pippeline.