Introduction to “Bacteria Density Analyzer”

1. Introduction

• Bacteria Density Analyzer is a Python module and a Napari plugin allowing to segment, skeletonize and extract a 1D signal from a 3D filament.

• It uses a segmentation channel (nuclei) and N fluorescence channels (bacteria) to compute the density of bacteria along the filaments.

• This module offers the possibility to have several filaments on the same image, even if they happen to be broken or if a region can’t be segmented.

• The output is a CSV file containing, for each filament, the density of bacteria along its length for each fluorescence channel.

• The plots corresponding to measures are also exported.

• Measures are made along a 1D skeleton and are binned according to a user-defined length.

2. Install the plugin

• We strongly recommend to use conda or any other virtual environment manager instead of installing Napari and bacteria-density in your system’s Python.

• Napari is only required if you want to use bacteria-density with a graphical interface.

• Napari is not part of bacteria-density’s dependencies, so you will have to install it separately.

• Each of the commands below is supposed to be run after you activated your virtual environment.

• If the install was successful, you should see the plugin in Napari in the top bar menu: Plugins > Density vs. distance.

A. Development versions

If you want to install a version from GitHub, you need to have Git installed on your computer.

Method	Instructions
Latest	pip install git+https://github.com/MontpellierRessourcesImagerie/bacteria-density.git
From an archive	Download the archive pyproject.toml and launch pip install -e .. From the terminal containing your virtual env, move to the folder containing the file pyproject.toml Run the command pip install -e .

B. Stable versions

Method	Instructions
pip	Activate your conda environment, and type pip install bacteria-density.