single cell RNA profiling analysis of imaging-based spatial transcriptomics data
Project description
ComSeg framework
A detail documentation is available Here https://comseg.readthedocs.io/en/latest/userguide.html
Single cell spatial RNA profiling
ComSeg is an algorithm for single cell spatial RNA profiling in image-based transcriptomic data.
It takes as input a csv with the spot coordinates and output an anndata object with the genes expression and coordinates of each cell.
Citation
A point cloud segmentation framework for image-based spatial transcriptomics 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
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