Tutorials
=========

MI Visium
----------

The following tutorials use data from the Myocardial Infarction (MI) atlas :cite:p:`kuppe_spatial_2022`. The first one demonstrates how NicheSphere identifies differential co-localization niches and associated biological processes related to ischemia. Then, the second one uses `PILOT <https://github.com/CostaLab/PILOT/>`_ to infer a disease trajectory at the sample level.


.. nbgallery::

    notebooks/Nichesphere_tutorial_MIvisium
    notebooks/Nichesphere_tutorial_MIvisium_PILOT


PIC-seq 
--------

The following tutorial applies NicheSphere to fibrosis mouse models (TPO) bone marrow PIC-seq data :cite:p:`gleitz_nichesphere_2026` to identify fibrosis specific co-localization niches and associated biological processes.

.. nbgallery::

    notebooks/Nichesphere_tutorial_BM_PICseq.ipynb


CODEX
------

The following tutorial applies NicheSphere to fibrosis mouse models (Ctrl, ThPO, MPL) spleen CODEX data :cite:p:`dugue_spatial_2026` to identify fibrosis specific co-localization niches. Then it uses `PILOT <https://github.com/CostaLab/PILOT/>`_ to infer a disease trajectory at the sample level.

.. nbgallery::

    notebooks/Nichesphere_tutorial_CODEX_PILOT.ipynb


Data required to run all the tutorials can be downloaded from Zenodo: https://doi.org/10.5281/zenodo.22678370