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Zonation image analysis

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This repository implements functionality for the image analysis based on whole-slide images (WSI) and large images either using brightfield or fluorescence microscopy. A key analysis is the analysis and quantification of zonation patterns from fluorscence images of the liver using double stainings with CYP2E1 and E-catharin.

Features include among others

• helper functions for reading and writing pyramidal formats (OME-TIF)
• tools for quantification of zonation patterns
• image processing helpers

.. image:: https://github.com/matthiaskoenig/zonation-image-analysis/raw/develop/docs/images/zonation.png :align: left :alt: zonation example

Installation

The analysis depends on the openslide library. Make sure this installed on your system, e.g. on linux via

sudo apt-get install openslide-tools

Install python package

The latest develop version can be installed from source via::

pip install git+https://github.com/matthiaskoenig/zonation-image-analysis.git@develop

Or via cloning the repository and installing via::

mkvirtualenv zonation --python=python3.10
git clone https://github.com/matthiaskoenig/zonation-image-analysis.git
cd zonation-image-analysis
pip install -e . --upgrade

For developing use::

pip install -e .[development] --upgrade

License

• Source Code: LGPLv3 <http://opensource.org/licenses/LGPL-3.0>__
• Documentation: CC BY-SA 4.0 <http://creativecommons.org/licenses/by-sa/4.0/>__

The zonation-image-analysis source is released under both the GPL and LGPL licenses version 2 or later. You may choose which license you choose to use the software under.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License or the GNU Lesser General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

Funding

Matthias König is supported by the Federal Ministry of Education and Research (BMBF, Germany) within the research network Systems Medicine of the Liver (LiSyM, grant number 031L0054) and by the German Research Foundation (DFG) within the Research Unit Programme FOR 5151 "QuaLiPerF <https://qualiperf.de>__ (Quantifying Liver Perfusion-Function Relationship in Complex Resection - A Systems Medicine Approach)" by grant number 436883643 and by grant number 465194077 (Priority Programme SPP 2311, Subproject SimLivA).

© 2022-2023 Jonas Küttner and Matthias König