Tutorials
=========

In our first example we will use data from the Myocardial Infarction atlas from Kuppe, C. et. Al., 2022 to find differential co-localization domains related to ischemia. The data you'll need to run the tutorials can be found here: https://doi.org/10.5281/zenodo.15790389  

.. nbgallery::
    :caption: Notebooks:
    :glob:

    notebooks/Nichesphere_tutorial_MIvisium_coloc.ipynb
    notebooks/Nichesphere_tutorial_MIvisium_comm.ipynb
    notebooks/Nichesphere_tutorial_MIvisium_preprocessing.ipynb

NicheSphere results can be used for condition to condition trajectory inference with PILOT https://github.com/CostaLab/PILOT . 

.. nbgallery::
    :caption: Notebooks:
    :glob:

    notebooks/Nichesphere-PILOT_integration_tutorial.ipynb