PyNutil
=======
a Python library for brain-wide quantification and spatial analysis of features in serial section images from the brain. 

.. grid:: 1 2 2 3
   :gutter: 3

   .. grid-item-card:: :fas:`book;sd-text-primary` Getting Started
      :link: getting_started
      :link-type: doc

      Installation, supported formats and key concepts.

   .. grid-item-card:: :fas:`desktop;sd-text-primary` GUI
      :link: gui
      :link-type: doc

      Use PyNutil via the graphical user interface.

   .. grid-item-card:: :fas:`images;sd-text-primary` Gallery
      :link: demos
      :link-type: doc

      A gallery of examples using PyNutil.

.. image:: ../assets/PyNutil_fig1.png
   :alt: Overview figure for the PyNutil workflow
   :width: 100%

Overview
----------
PyNutil is able to integrate outputs from various atlas registration software and image segmentation software in order 
to produce atlas based quantifications, 3D point clouds, and 3D heatmaps of brain derived data. 

PyNutil aims to replicate and expand the Quantifier feature of the Nutil software (RRID: SCR_017183). 

.. warning::

   PyNutil is still under development and the API is subject to change.

The documentation below brings together installation notes, the basic workflow,
practical examples, and the generated API reference.

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

   getting_started
   gui
   demos
   api_index

Highlights
----------

* Use BrainGlobe atlases or custom atlas volumes in ``.nrrd`` format.
* Read registration data from QuickNII, VisuAlign, DeepSlice, or
  BrainGlobe registration outputs.
* Quantify binary segmentations or intensity images against atlas regions.
* Export point clouds for MeshView and interpolated NIfTI volumes for
  siibra explorer or ITK-SNAP.

For more background on the QUINT workflow, see
`QUINT workflow documentation <https://quint-workflow.readthedocs.io/en/latest/>`_.

Index & Search
--------------

* :ref:`genindex`
* :ref:`search`