What is sainsc?
===================

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sainsc (pronounced /ˈsaiəns/|audio_science|, 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 <https://github.com/scverse>`_
(i.e., `scanpy` and `squidpy`) by exporting data in
`AnnData <https://anndata.readthedocs.io/>`_ or
`SpatialData <https://spatialdata.scverse.org/>`_ format.

Citations
---------

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 <https://doi.org/10.1002/smtd.202401123>`_

.. toctree::
   :maxdepth: 2
   :caption: Contents:

   self
   quickstart
   installation
   tutorials/index