Metadata-Version: 2.1
Name: biapol-utilities
Version: 0.0.3
Summary: Collection of bio-image analysis functions of the biapol group @ TU Dresden.
Home-page: https://github.com/BiAPoL/biapol-utilities.git
Author: Johannes Müller, Robert Haase
Author-email: johannes_richard.mueller@tu-dresden.de
License: BSD-3-Clause
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: Topic :: Software Development :: Testing
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Operating System :: OS Independent
Classifier: License :: OSI Approved :: BSD License
Requires-Python: >=3.7
Description-Content-Type: text/markdown
License-File: LICENSE

# biapol-utilities
[![Python Version](https://img.shields.io/pypi/pyversions/biapol-utilities.svg?color=green)](https://python.org)
[![test](https://github.com/BiAPoL/biapol-utilities/actions/workflows/test.yml/badge.svg)](https://github.com/BiAPoL/biapol-utilities/actions/workflows/test.yml)
[![Contributors](https://img.shields.io/github/contributors-anon/BiAPoL/biapol-utilities)](https://github.com/BiAPoL/biapol-utilities/graphs/contributors)
[![codecov](https://codecov.io/gh/BiAPoL/biapol-utilities/branch/master/graph/badge.svg)](https://codecov.io/gh/BiAPoL/biapol-utilities)

Collection of utility functions from the BiA-PoL group at the DFG Cluster of Excellence "Physics of Life" (PoL) @ TU Dresden, Germany. 

## Usage 

This library contains functions for comparing and visualizing label images. For example, comparing label images is as easy as this:
```python
import biapol_utilities as biau

biau.label.compare_labels(ground_truth, segmented)
```
![img.png](https://github.com/BiAPoL/biapol-utilities/raw/main/docs/_static/example_table.png?raw=true)

In another example, you can visualize a label image with a nice color map like this:

```python
import biapol_utilities as biau
from skimage.io import imshow

imshow(label_image, cmap=biau.labels_colormap(), vmin=0, vmax=labels.max())
```
![img.png](https://github.com/BiAPoL/biapol-utilities/raw/main/docs/_static/example_label_image.png?raw=true)

We provide examples to most of our functionality on our [documentation](https://biapol.github.io/biapol-utilities/_include/Examples.html). The examples are also available as [jupyter notebooks](https://github.com/BiAPoL/biapol-utilities/tree/main/docs/_include/notebooks/label).

## Installation

`biapol-utilities` can be installed using pip:

`pip install biapol-utilities`

If you want to develop `biapol-utilities` you can download and install it like this:

```
git clone https://github.com/BiAPoL/biapol-utilities
cd biapol-utilities
pip install -e .
```

## Ressources

* [Documentation](https://biapol.github.io/biapol-utilities)
* [Source code](https://github.com/BiAPoL/biapol-utilities)
* [Bug reports are welcome here](https://github.com/BiAPoL/biapol-utilities/issues)
* [How to contribute](https://biapol.github.io/biapol-utilities/_include/Contribute.html)

## Acknowledgements
Developing biapol-utilities is a community effort. We would like to thank everybody who helped developing and testing. 
Furthermore, we are gladly re-using code from other open source projects. 
See the the [thirdparty-licenses folder](https://github.com/BiAPoL/biapol-utilities/tree/main/license_thirdparty) for details.


