SimBA

Note

These docs are under active development. For detailed tutorials, code, and more extensive documentation, see the SimBA GitHub repository.

💻 GitHub 📦 PyPI 📄 Paper 📑 Cite SimBA 💬 Gitter support 🎥 Watch the overview

🚀 INSTALLATION

To install SimBA from PyPI, run the following (use Python 3.6, or 3.10 if necessary):

pip install simba-uw-tf-dev

Then launch it by typing simba. For step-by-step setup — conda, Anaconda Navigator, or video walkthroughs — see the full installation guide:

⚙️ Full installation guide 📖 Install guide on GitHub

📑 HOW TO CITE SIMBA

Using SimBA in your research? Please cite the SimBA paper:

Nature Neuroscience · 2024 · 27(7), 1411–1424

Simple Behavioral Analysis (SimBA) as a platform for explainable machine learning in behavioral neuroscience

Goodwin, N. L., Choong, J. J., Hwang, S., et al. … Nilsson, S. R. O., & Golden, S. A.

Goodwin, N. L., Choong, J. J., Hwang, S., Pitts, K., Bloom, L., Islam, A., Zhang, Y. Y., Szelenyi, E. R., Tong, X., Newman, E. L., Miczek, K., Wright, H. R., McLaughlin, R. J., Norville, Z. C., Eshel, N., Heshmati, M., Nilsson, S. R. O., & Golden, S. A. (2024). Simple Behavioral Analysis (SimBA) as a platform for explainable machine learning in behavioral neuroscience. Nature Neuroscience, 27(7), 1411–1424. https://doi.org/10.1038/s41593-024-01649-9

Goodwin, Nastacia L., et al. “Simple Behavioral Analysis (SimBA) as a Platform for Explainable Machine Learning in Behavioral Neuroscience.” Nature Neuroscience, vol. 27, no. 7, 2024, pp. 1411–24, https://doi.org/10.1038/s41593-024-01649-9.

Goodwin, Nastacia L., Jia J. Choong, Sophia Hwang, Kayla Pitts, Liana Bloom, Aasiya Islam, Yizhe Y. Zhang, et al. “Simple Behavioral Analysis (SimBA) as a Platform for Explainable Machine Learning in Behavioral Neuroscience.” Nature Neuroscience 27, no. 7 (2024): 1411–24. https://doi.org/10.1038/s41593-024-01649-9.

Goodwin, N.L. et al. (2024) ‘Simple Behavioral Analysis (SimBA) as a platform for explainable machine learning in behavioral neuroscience’, Nature Neuroscience, 27(7), pp. 1411–1424. Available at: https://doi.org/10.1038/s41593-024-01649-9.

Goodwin NL, Choong JJ, Hwang S, Pitts K, Bloom L, Islam A, et al. Simple Behavioral Analysis (SimBA) as a platform for explainable machine learning in behavioral neuroscience. Nat Neurosci. 2024;27(7):1411–24. doi:10.1038/s41593-024-01649-9

@article{Goodwin_2024,
  title     = {Simple Behavioral Analysis (SimBA) as a platform for explainable machine learning in behavioral neuroscience},
  author    = {Goodwin, Nastacia L. and Choong, Jia J. and Hwang, Sophia and Pitts, Kayla and Bloom, Liana and Islam, Aasiya and Zhang, Yizhe Y. and Szelenyi, Eric R. and Tong, Xiaoyu and Newman, Emily L. and Miczek, Klaus and Wright, Hayden R. and McLaughlin, Ryan J. and Norville, Zane C. and Eshel, Neir and Heshmati, Mitra and Nilsson, Simon R. O. and Golden, Sam A.},
  journal   = {Nature Neuroscience},
  volume    = {27},
  number    = {7},
  pages     = {1411--1424},
  year      = {2024},
  doi       = {10.1038/s41593-024-01649-9},
  url       = {https://doi.org/10.1038/s41593-024-01649-9},
  publisher = {Springer Science and Business Media LLC}
}

TY  - JOUR
AU  - Goodwin, Nastacia L.
AU  - Choong, Jia J.
AU  - Hwang, Sophia
AU  - Pitts, Kayla
AU  - Bloom, Liana
AU  - Islam, Aasiya
AU  - Zhang, Yizhe Y.
AU  - Szelenyi, Eric R.
AU  - Tong, Xiaoyu
AU  - Newman, Emily L.
AU  - Miczek, Klaus
AU  - Wright, Hayden R.
AU  - McLaughlin, Ryan J.
AU  - Norville, Zane C.
AU  - Eshel, Neir
AU  - Heshmati, Mitra
AU  - Nilsson, Simon R. O.
AU  - Golden, Sam A.
TI  - Simple Behavioral Analysis (SimBA) as a platform for explainable machine learning in behavioral neuroscience
JO  - Nature Neuroscience
VL  - 27
IS  - 7
SP  - 1411
EP  - 1424
PY  - 2024
DO  - 10.1038/s41593-024-01649-9
UR  - https://doi.org/10.1038/s41593-024-01649-9
ER  -

📄 Read the paper 🔗 DOI ⬇ .bib ⬇ .ris 🎓 Google Scholar

The .ris file imports into Mendeley, EndNote, Zotero and most other reference managers. You can also paste the DOI (10.1038/s41593-024-01649-9) into your manager's “add by identifier” option.

SimBA works alongside other open-source tools. Please also cite the pose-estimation software and any other packages your analysis used.