Update with comseg 0.0.7. Computation if the co-expression matrix is now faster.
If you have any questions relative to the package or bug, please open an issue in this repository.
A detail documentation is available Here https://comseg.readthedocs.io/en/latest/userguide.html
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.
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