.. WSITools documentation master file, created by

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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`