MotilA documentation
====================

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`MotilA <https://github.com/FabrizioMusacchio/MotilA>`_ is a Python-based pipeline for microglial fine process motility analysis
from 4D and 5D multiphoton imaging data.


.. figure:: _static/figures/all_stacks_4D_reg_cut_out_MotilA_example_small.gif
   :alt: MotilA pipeline overview
   :align: center
   :figwidth: 100%

   **MotilA's segmentation and 
   microglial turnover rate assessment**. This animation illustrates the structural 
   changes that MotilA detects and quantifies. The left panel shows one representative 
   Z-slice per time point after MotilA's internal preprocessing steps. The right panel 
   shows the corresponding :math:`\Delta B` classification maps, which are computed as 
   difference images between two consecutive time points :math:`t_i` and :math:`t_{i+1}`.


This documentation provides:

* an overview of the pipeline and its scientific context,
* installation and basic usage instructions,
* a detailed description of the processing steps and parameters,
* an automatically generated API reference.

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

   overview
   data_requirements
   tutorials
   parameters
   api
   contributing

MotilA is `free and open-source software (FOSS) <https://en.wikipedia.org/wiki/Free_and_open-source_software>`_ distributed under the :ref:`GPL-3.0 license <license>`.