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SSAM Example Jupyter Notebooks

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.

Note:

  • To replicate the results in this repo, please use the package python-louvain == 0.13 (The newer version, python-louvain 0.14, uses a different randomization algorithm).

Supplemental Data

The supplemental data used in the notebooks can be automatically downloaded using the script download_data.sh.

Citations

Jeongbin Park, Wonyl Choi, Sebastian Tiesmeyer, Brian Long, Lars E. Borm, Emma Garren, Thuc Nghi Nguyen, Bosiljka Tasic, Simone Codeluppi, Tobias Graf, Matthias Schlesner, Oliver Stegle, Roland Eils & Naveed Ishaque. "Cell segmentation-free inference of cell types from in situ transcriptomics data." Nature Communications 12, 3545 (2021).