single cell RNA profiling analysis of imaging-based spatial transcriptomics data
Project description
News (16/07/24)
- Update with comseg 1.4: Compatibility with SOPA : (https://gustaveroussy.github.io/sopa/tutorials/comseg/) + fix bug centroid
Support
If you have any questions relative to the package or bug, please open an issue in this repository.
ComSeg framework
A detail documentation is available at https://comseg.readthedocs.io/
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
Defard, T., Laporte, H., Ayan, M. et al. A point cloud segmentation framework for image-based spatial transcriptomics. Commun Biol 7, 823 (2024). https://doi.org/10.1038/s42003-024-06480-3
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