# 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
```bash
conda env create -f conda_env.yaml
conda activate behavysis_viewer_env
pip install poetry
poetry install
```
### User installation
```bash
conda env create -f conda_env.yaml
```
## Running
```bash
behavysis_viewer
```
```bash
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
Raw data
{
"_id": null,
"home_page": "https://tlee08.github.io/behavysis_viewer",
"name": "behavysis_viewer",
"maintainer": null,
"docs_url": null,
"requires_python": "<4.0,>=3.12",
"maintainer_email": null,
"keywords": null,
"author": "BowenLab",
"author_email": null,
"download_url": "https://files.pythonhosted.org/packages/c0/69/031b1bb23c3413bdf6f5cb6bd8ba5bef574e63a9ba149e839fadb419cb92/behavysis_viewer-0.1.20.tar.gz",
"platform": null,
"description": "# behavysis_viewer\n\nSemi-automated scoring animal behaviour. Behaviour is first predicted by a classifier and then the user verifies & further scores this behaviour.\n\n## Installation\n\n### Dev installation\n\n```bash\nconda env create -f conda_env.yaml\nconda activate behavysis_viewer_env\npip install poetry\npoetry install\n```\n\n### User installation\n\n```bash\nconda env create -f conda_env.yaml\n```\n\n## Running\n\n```bash\nbehavysis_viewer\n```\n\n```bash\npyside6-uic behavysis_viewer/ui/main_ui.ui -o behavysis_viewer/ui/main_ui.py\n\npyside6-uic behavysis_viewer/ui/settings_ui.ui -o behavysis_viewer/ui/settings_ui.py\n```\n\n## References\n\nMathis, 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\n\nNath, 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\n\nLauer, J., Zhou, M., Ye, S., Menegas, W., Schneider, S., Nath, T., \u2026 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\n\nNilsson, 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\n",
"bugtrack_url": null,
"license": "LGPL-3.0-or-later",
"summary": "A semi-automated behaviour verification, processing and analysis package.",
"version": "0.1.20",
"project_urls": {
"Homepage": "https://tlee08.github.io/behavysis_viewer",
"Repository": "https://github.com/tlee08/behavysis_viewer"
},
"split_keywords": [],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "ca0813d15b8bd32e1883aa3d3a7de543faf1100d39bee8b6e23bffdf9379a0f6",
"md5": "a218a1ea11f011350be485462bc24137",
"sha256": "c9303abb5e27fc1ad89af887d604bc40711d3660a4809d15ced59a147c0e8283"
},
"downloads": -1,
"filename": "behavysis_viewer-0.1.20-py3-none-any.whl",
"has_sig": false,
"md5_digest": "a218a1ea11f011350be485462bc24137",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": "<4.0,>=3.12",
"size": 41928,
"upload_time": "2024-08-16T07:38:23",
"upload_time_iso_8601": "2024-08-16T07:38:23.985124Z",
"url": "https://files.pythonhosted.org/packages/ca/08/13d15b8bd32e1883aa3d3a7de543faf1100d39bee8b6e23bffdf9379a0f6/behavysis_viewer-0.1.20-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "c069031b1bb23c3413bdf6f5cb6bd8ba5bef574e63a9ba149e839fadb419cb92",
"md5": "a323aa2a1d629bc19ea202b40a9192d7",
"sha256": "3acb2148b7804fee8c2e87380953c3ce5481f6df5c27b7facdac4a328dd83bf7"
},
"downloads": -1,
"filename": "behavysis_viewer-0.1.20.tar.gz",
"has_sig": false,
"md5_digest": "a323aa2a1d629bc19ea202b40a9192d7",
"packagetype": "sdist",
"python_version": "source",
"requires_python": "<4.0,>=3.12",
"size": 34933,
"upload_time": "2024-08-16T07:38:25",
"upload_time_iso_8601": "2024-08-16T07:38:25.795459Z",
"url": "https://files.pythonhosted.org/packages/c0/69/031b1bb23c3413bdf6f5cb6bd8ba5bef574e63a9ba149e839fadb419cb92/behavysis_viewer-0.1.20.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2024-08-16 07:38:25",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "tlee08",
"github_project": "behavysis_viewer",
"travis_ci": false,
"coveralls": false,
"github_actions": false,
"lcname": "behavysis_viewer"
}
JSON
