A package for bacterial image processing
Project description
BactoVision
A jupyter widget for annotating and visualizing bacterial growth data
Bactovision provides a widget for jupyter notebook for fast semi-automated annotation of bacterial growth images. It is used in the following paper:
Tyrosine auxotrophy shapes Staphylococcus aureus nasal colonization and interactions with commensal communities L. Camus et al. 2025 (submitted)
Installation
Use pip to install the package:
pip install bactovision
or install from source:
git clone git@github.com:StarostinV/bactovision.git
cd bactovision
pip install .
That will install the package along with the following dependencies:
- numpy
- scipy
- scikit-image
- Pillow
- opencv-python
- anywidget
- traitlets
- matplotlib
- jupyterlab
Documentation
Please see the documentation here.
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