This repository contains SSAM examples of three mouse brain tissue samples:
- Primary somatosensory cortex (SSp) imaged by osmFISH
- Hypothalamus preoptic region (POA) imaged by MERFISH
- Primary visual cortex (VISp) imaged by multiplexed smFISH
And the diagnostic plots could be found in the following three directories: diagplots_osmFISH, diagplots_MERFISH, and diagplots_multiplexed_smFISH.
The supplemental data used in the notebooks can be automatically downloaded using the script download_data.sh.
J Park, W Choi, S Tiesmeyer, B Long, LE Borm, E Garren, TN Nguyen, S Codeluppi, M Schlesner, B Tasic, R Eils, N Ishaque. "Segmentation-free inference of cell types from in situ transcriptomics data." bioRxiv 800748. doi: https://doi.org/10.1101/800748