Metadata-Version: 2.1
Name: ComSeg
Version: 1.5.dev0
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
Requires-Dist: anndata>=0.9.2
Requires-Dist: h5py>=3.9.0
Requires-Dist: networkx>=2.8.4
Requires-Dist: numba>=0.55.2
Requires-Dist: numpy>=1.22.4
Requires-Dist: pandas>=1.4.0
Requires-Dist: Pillow>=10.0.1
Requires-Dist: pyarrow>=13.0.0
Requires-Dist: rpds-py>=0.10.3
Requires-Dist: scanpy>=1.9.5
Requires-Dist: scikit-image>=0.21.0
Requires-Dist: scikit-learn>=1.0.1
Requires-Dist: scikit-misc>=0.2.0
Requires-Dist: scipy>=1.8.1
Requires-Dist: seaborn>=0.12.2
Requires-Dist: tifffile>=2023.7.10
Requires-Dist: tinycss2>=1.2.1
Requires-Dist: tqdm>=4.66.1
Requires-Dist: traitlets>=5.11.2
Requires-Dist: umap-learn>=0.5.4
Requires-Dist: webencodings>=0.5.1
Requires-Dist: zipp>=3.16.2
Requires-Dist: alphashape>=1.3.1
Requires-Dist: igraph>=0.11.5
Requires-Dist: leidenalg>=0.10.2


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

# 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


