Metadata-Version: 2.1
Name: ComSeg
Version: 0.4
Summary: single cell RNA profiling analysis of imaging-based spatial transcriptomics data
Author-email: Thomas Defard <thomas.defard@mines-paristech.fr>
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE


<img src="./comseg.png" width="650" height="263">

# News
- Update with comseg 0.0.8. Compatibility with SOPA : https://gustaveroussy.github.io/sopa/

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

# 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 

A point cloud segmentation framework for image-based spatial transcriptomic, Defard et al bioRxiv 2023.12.01.569528; doi: https://doi.org/10.1101/2023.12.01.569528

