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 [email protected]:mlcolab/bactovision.git
cd bactovision
pip install .

Documentation

Please see the full documentation here.

Basic usage

Start a jupyter notebook:

jupyter notebook

In the notebook, create a widget:

from bactovision import BactoWidget

# Create a widget with an image
widget = BactoWidget('path/to/image.png')

# Display the widget
widget

To get the mask and the metrics after the annotation is completed, run:

annotation_mask = widget.get_annotation_mask()
metrics = widget.get_metrics()