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+.. 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`