behavysis_viewer 0.1.3

A semi-automated behaviour verification, processing and analysis package.

behavysis_viewer

Semi-automated scoring animal behaviour. Behaviour is first predicted by a classifier and then the user verifies & further scores this behaviour.

Installation

Dev installation

conda env create -f conda_env.yaml
conda activate behavysis_viewer_env
pip install poetry
poetry install

User installation

conda env create -f conda_env.yaml

Running

behavysis_viewer

pyside6-uic behavysis_viewer/ui/main_ui.ui -o behavysis_viewer/ui/main_ui.py

pyside6-uic behavysis_viewer/ui/settings_ui.ui -o behavysis_viewer/ui/settings_ui.py

References

Mathis, A., Mamidanna, P., Cury, K. M., Abe, T., Murthy, V. N., Mathis, M. W., & Bethge, M. (2018, August 20). DeepLabCut: markerless pose estimation of user-defined body parts with deep learning. Nature Neuroscience. Springer Science and Business Media LLC. http://doi.org/10.1038/s41593-018-0209-y

Nath, T., Mathis, A., Chen, A. C., Patel, A., Bethge, M., & Mathis, M. W. (2019, June 21). Using DeepLabCut for 3D markerless pose estimation across species and behaviors. Nature Protocols. Springer Science and Business Media LLC. http://doi.org/10.1038/s41596-019-0176-0

Lauer, J., Zhou, M., Ye, S., Menegas, W., Schneider, S., Nath, T., … Mathis, A. (2022, April). Multi-animal pose estimation, identification and tracking with DeepLabCut. Nature Methods. Springer Science and Business Media LLC. http://doi.org/10.1038/s41592-022-01443-0

Nilsson, S., Goodwin, N., Choong, J. J., Hwang, S., Wright, H., Norville, Z., Tong, X., Lin, D., Bentzley, B., Eshel, N., McLaughlin, R., & Golden, S. Simple Behavioral Analysis (SimBA): an open source toolkit for computer classification of complex social behaviors in experimental animals [Computer software]. https://github.com/sgoldenlab/simba