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https://github.com/Bayer-Group/paquo

PAthological QUpath Obsession - QuPath and Python conversations
https://github.com/Bayer-Group/paquo

digital-pathology python qupath

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PAthological QUpath Obsession - QuPath and Python conversations

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README 

        
# PAQUO: PAthological QUpath Obsession



[![PyPI Version](https://img.shields.io/pypi/v/paquo)](https://pypi.org/project/paquo/)

[![Conda (channel only)](https://img.shields.io/conda/vn/conda-forge/paquo?label=conda)](https://anaconda.org/conda-forge/paquo)

[![Read the Docs](https://img.shields.io/readthedocs/paquo)](https://paquo.readthedocs.io)

[![paquo ci](https://github.com/bayer-science-for-a-better-life/paquo/actions/workflows/run_pytests.yaml/badge.svg?branch=main)](https://github.com/bayer-science-for-a-better-life/paquo/actions/workflows/run_pytests.yaml)

[![Codecov](https://img.shields.io/codecov/c/github/bayer-science-for-a-better-life/paquo)](https://codecov.io/gh/bayer-science-for-a-better-life/paquo)

[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/paquo)](https://github.com/bayer-science-for-a-better-life/paquo)

[![GitHub issues](https://img.shields.io/github/issues/bayer-science-for-a-better-life/paquo)](https://github.com/bayer-science-for-a-better-life/paquo/issues)



Welcome to `paquo` :wave:, a library for interacting with [QuPath](https://qupath.github.io/)

from [Python](https://www.python.org/).



`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](https://github.com/bayer-science-for-a-better-life/paquo)

:octocat:



## Documentation



You can find `paquo`'s documentation at

[paquo.readthedocs.io](https://paquo.readthedocs.io) :heart:



## Installation



paquo's stable releases can be installed via `pip`:

```bash

pip install paquo

```



or via `conda`:

```bash

conda install -c conda-forge paquo

```



## Getting QuPath



After installing, paquo requires a QuPath installation to run. To get QuPath follow the

[installation instructions](https://qupath.readthedocs.io/en/stable/docs/intro/installation.html).

If you choose the default installation paths paquo should autodetect your QuPath.



Or you can run the following command to download a specific version of QuPath

to a location on your machine. Follow the printed instructions to configure

paquo to use that version. Currently, paquo supports every version of QuPath from

`0.2.0` to the most recent. _(We even support older `0.2.0-mX` versions but no guarantees)._



```shell

> paquo get_qupath --install-path "/some/path/on/your/machine" 0.5.0

# downloading: https://github.com/qupath/qupath/releases/download/v0.5.0/QuPath-0.4.3-Linux.tar.xz

# progress ................... OK

# extracting: [...]/QuPath-0.5.0-Linux.tar.xz

# available at: /some/path/on/your/machine/QuPath-0.5.0

#

# use via environment variable:

#   $ export PAQUO_QUPATH_DIR=/some/path/on/your/machine/QuPath-0.5.0

#

# use via .paquo.toml config file:

#   qupath_dir="/some/path/on/your/machine/QuPath-0.5.0"

/some/path/on/your/machine/QuPath-0.5.0

```



## Development Installation



1. Install conda and git

2. Clone paquo `git clone https://github.com/bayer-science-for-a-better-life/paquo.git`

3. Run `conda env create -f environment.devenv.yaml`

4. 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](https://www.python.org/dev/peps/pep-0008/) but:

  - We allow 120 character long lines (try anyway to keep them short)

- Please use [numpy docstrings](https://numpydoc.readthedocs.io/en/latest/format.html#docstring-standard).

- When contributing code, please try to use Pull Requests.

- tests go hand in hand with modules on ```tests``` packages at the same level. We use ```pytest```.



You can set up your IDE to help you to adhere to these guidelines.




_([Santi](https://github.com/sdvillal) is happy to help you to set 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](https://github.com/bayer-science-for-a-better-life/paquo/blob/master/LICENSE)