sainsc (pronounced /ˈsaiəns/ 🔊 , i.e., 'science') is a segmentation-free analysis tool for spatial transcriptomics from in situ capture technologies (but also works for imaging-based technologies).
It is easily integratable with the scverse (i.e., scanpy and squidpy) by exporting data in AnnData or SpatialData format.
If you are using sainsc for your research, please cite
N. Müller-Bötticher, S. Tiesmeyer, R. Eils, N. Ishaque, "Sainsc: A Computational Tool for Segmentation-Free Analysis of In Situ Capture Data" Small Methods 9, 2401123 (2025) doi: 10.1002/smtd.202401123
.. toctree:: :maxdepth: 2 :caption: Contents: self quickstart installation tutorials/index