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BiAPoL / biapol-utilities

Collection of utility functions from the Bio-image Analysis Technology Development group at the DFG Cluster of Excellence "Physics of Life", TU Dresden, Dresden, Germany
BSD 3-Clause "New" or "Revised" License
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biapol-utilities

Python Version test Contributors codecov

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:

import biapol_utilities as biau

biau.label.compare_labels(ground_truth, segmented)

img.png

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

import biapol_utilities as biau
from skimage.io import imshow

imshow(label_image, cmap=biau.labels_colormap(), vmin=0, vmax=labels.max())

img.png

We provide examples to most of our functionality on our documentation. The examples are also available as jupyter notebooks.

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

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 for details.