physbeh 0.6.4

Miscellaneous functions for tracking analysis in Python using DeepLabCut at Physics for Medicine

PhysBeh

This repository contains the main function and classes written in Python for analysis of tracking data in the Physics for Medicine lab.

The code is written in the format of a Python package (physbeh).

This is the core package used for the behavioral analysis in the following paper:

1. Cybis Pereira, F., Castedo, S.H., Meur-Diebolt, S.L., Ialy-Radio, N., Bhattacharya, S., Ferrier, J., Osmanski, B.F., Cocco, S., Monasson, R., Pezet, S., et al. (2026). A vascular code for speed in the spatial navigation system. Cell Reports 45. https://doi.org/10.1016/j.celrep.2025.116791.

Installation

1. Setup a virtual environment

Create and activate a new python environment (if familiarisation with virtual environments is needed, you can start here or here):

• Using venv (recommended):

  On Linux

  python3 -m venv /path_to_env
  source /path_to_env/bin/activate

  On Windows

  python3 -m venv /path_to_env
  /path_to_env/Script/activate

• Using conda:

  conda create -n physbeh python=3.11
  conda activate physbeh

2. Install PhysBeh from source

PhysBeh is a private package developed by Iconeus and Physics for Medicine and is not available from PyPI.

python -m pip install git+https://github.com/FelipeCybis/physbeh.git

3. Check installation

Check that all tests pass:

import physbeh

If no error is raised, you have installed PhysBeh correctly.

Authors

• Felipe Cybis Pereira ([e-mail])