.. WSITools documentation master file, created by
   sphinx-quickstart.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

WSITools documentation!
==============================================

Tools to aid Digital pathology deep learning projects   

- Free software: MIT license
- Documentation: https://wsitools.readthedocs.io/en/latest/index.html

Features
--------
WSITools is a whole slide image processing toolkit. It provides efficient ways to extract patches from whole slide 
images, and some other useful features for pathological image processing.
Currently, it supports four patch extraction scenarios:
..  1. Extract patches from WSIs
..  2. Extract patches from WSIs and their label (i.e. their directory name)
..   1. TODO: Incomplete
..  3. Extract patches from a fixed and a float WSI
..  4. Extract patches from a fixed and a float WSI in places that intersect annotation objects
..   1. TODO: Incomplete

Additional Features
-------------------
..  1. Detect tissue in a WSI
..  2. Export and parsing annotation from [QuPath_] and [`Aperio Image Scope`_] 
..  3. WSI registration for image pairs [Paper_]
..  4. Reconstruct WSI from the processed image patches

.. _QuPath: https://qupath.github.io
.. _Aperio Image Scope: https://www.leicabiosystems.com/digital-pathology/manage/aperio-imagescope
.. _Paper: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0220074

Contents:

.. toctree::
   :maxdepth: 2

   getting-started
   example-commands
   Tissue-Detection
   Patch-Extraction
   Patch-Extraction-with-Registration
   Patch-Extraction-with-Annotation
   Patch-Extraction-with-Registration-and-Annotation
   
	


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

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