.. based on NumPy's documentation

.. _sarcgraph_docs_mainpage:

.. toctree::
   :maxdepth: 1
   :hidden:

   Getting Started <installation>
   Demos and Tutorials <tutorial/index>
   API Reference <reference/index>
   For Developers <dev_guide>

#######################
SarcGraph documentation
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**SarcGraph** is a tool for automatic detection, tracking and analysis of
z-discs and sarcomeres in movies of beating *human induced pluripotent stem
cell-derived cardiomyocytes (hiPSC-CMs)*.

Overview
--------

**SarcGraph** was initially introduced in
`"Sarc-Graph: Automated segmentation, tracking, and analysis of sarcomeres in
hiPSC-derived cardiomyocytes" <https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009443>`_.
This package is created to make **SarcGraph** more accessible to the broader
research community.

SarcGraph vs legacy Sarc-Graph
------------------------------

This package is the new version of the `legacy Sarc-Graph <https://github.com/elejeune11/Sarc-Graph>`_ 
library. The new `SarcGraph <https://github.com/Sarc-Graph/sarcgraph>`_ offers 
significant enhancements over its predecessor, such as new algorithms for 
improved sarcomere detection and tracking, faster computation times, and a more 
user-friendly library design.

Key Features
------------

**SarcGraph** includes functions to detect and track z-discs and sarcomeres in
beating cells, construct spatial graphs of z-discs and sarcomeres for network
distance computation, and perform automated spatiotemporal analysis and data
visualization.

.. grid:: 2
   
   .. grid-item-card::

      Getting Started
      ^^^^^^^^^^^^^^^
      
      How to install **SarcGraph**

      +++

      .. button-ref:: installation_ref
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         :color: secondary
         :click-parent:

         To installation guide
   
   .. grid-item-card::

      Demos & tutorials
      ^^^^^^^^^^^^^^^^^
      
      Check out demos and tutorials that contain introduction to all features 
      of **SarcGraph**

      +++

      .. button-ref:: demos_ref
         :expand:
         :color: secondary
         :click-parent:

         To demos and tutorials

   .. grid-item-card::

      API reference
      ^^^^^^^^^^^^^

      The reference guide contains a detailed description of the **SarcGraph**
      API.

      +++

      .. button-ref:: sarcgraph_api_ref
         :expand:
         :color: secondary
         :click-parent:

         To reference guide

   .. grid-item-card::

      For developers
      ^^^^^^^^^^^^^^

      The reference guide contains a detailed description of the **SarcGraph**
      API.

      +++

      .. button-ref:: dev_ref
         :expand:
         :color: secondary
         :click-parent:

         To develper's guide