library for interacting with QuPath
Project description
PAQUO: PAthological QUpath Obsession
Welcome to paquo
:wave:, a library for interacting with QuPath
from Python.
paquo
's goal is to provide a pythonic interface to important features of
QuPath, and to make creating and working with QuPath projects intuitive for
Python programmers.
We strive to make your lives as easy as possible: If paquo
is not pythonic,
unintuitive, slow or if its documentation is confusing, it's a bug in
paquo
. Feel free to report any issues or feature requests in the issue
tracker!
Development happens on github :octocat:
Documentation
You can find paquo
's documentation at
paquo.readthedocs.io :heart:
Development Installation
- Install conda and git
- Clone paquo
git clone https://github.com/bayer-science-for-a-better-life/paquo.git
- Run
conda env create -f environment.yaml
- Activate the environment
conda activate paquo
Note that in this environment paquo
is already installed in development mode,
so go ahead and hack.
Contributing Guidelines
- Please follow pep-8 conventions but:
- We allow 120 character long lines (try anyway to keep them short)
- Please use numpy docstrings.
- When contributing code, please try to use Pull Requests.
- tests go hand in hand with modules on
tests
packages at the same level. We usepytest
.
You can setup your IDE to help you adhering to these guidelines.
(Santi is happy to help you setting up pycharm in 5 minutes)
Acknowledgements
Build with love by Andreas Poehlmann and Santi Villalba from the Machine Learning Research group at Bayer. In collaboration with the Pathology Lab 2 and the Mechanistic and Toxicologic Pathology group.
paquo
: copyright 2020 Bayer AG, licensed under GPL-3.0
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