Welcome to ComSeg’s documentation!

ComSeg is an algorithm to perform cell segmentation from RNA point clouds (single cell spatial RNA profiling) from FISH based spatial transcriptomic data

It takes as input csv files with the spot coordinates and either the cell centroids or the nucleus segmentation masks. it outputs an anndata object with the genes expression and coordinates of each cell. It can leverage the information of the cell nuclei to improve the accuracy of the segmentation / RNA profiling.

News (16/07/24)

• Update with comseg 1.4: Compatibility with SOPA : (https://gustaveroussy.github.io/sopa/tutorials/comseg/) + fix bug centroid

• Update with comseg 0.0.7. Computation of the co-expression matrix is now faster.

Contents:

• Installation guide
  • Getting started
  • Support
• User guide
  • ComSeg tutorial
  • Minimal example : run ComSeg with a config dictionary
  • ComSeg on large scale data with SOPA / SpatialData
• Module comseg
  • Dataset
  • Graph model
  • ComSegDict
  • In-situ clustering

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Support

If you have any questions relative to the package, please open an issue on Github.

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Citation

If you use this package for your work, please cite:

A point cloud segmentation framework for image-based spatial transcriptomic, Thomas Defard, Hugo Laporte, Mallick Ayan, Soulier Juliette, Sandra Curras-Alonso, Christian Weber, Florian Massip, José-Arturo Londoño-Vallejo, Charles Fouillade, Florian Mueller, Thomas Walter bioRxiv 2023.12.01.569528; doi: https://doi.org/10.1101/2023.12.01.569528