.. Atlas Alignment documentation master file, created by
   sphinx-quickstart on Wed Oct 30 16:22:27 2019.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

Atlas Alignment
================
The goal of this project is to facilitate the registration of gene expression images to a reference (Nissl) atlas.

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

   source/installation
   source/image_registration
   source/building_blocks
   source/datasets
   source/intensity
   source/labeling_tool
   source/deep_learning_data
   source/deep_learning_training
   source/deep_learning_inference
   source/evaluation
   source/3d_interpolation

.. toctree::
   :maxdepth: 2
   :caption: API Reference

   source/api/modules



Indices and tables
==================

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