BentoMAT
A gui for browsing joint calcium imaging + behavioral data.
Install / Use
/learn @neuroethology/BentoMATREADME
Behavior Ensemble and Neural Trajectory Observatory
Bento is a Matlab GUI for managing multimodal neuroscience datasets. It lets you browse and annotate behavioral and neural data, train behavior classifiers, and helps you organize and navigate trials within a batch of experiments.
<div align=center> <b>Visit the <a href=https://github.com/annkennedy/bento/wiki>Bento Wiki</a> for documentation and tutorials</b> | <b>Watch our <a href=https://www.youtube.com/watch?v=mUQ4kDDPc_s>Demo Video</a> on Youtube</b></div> <br><br> <div align=center> <img src='https://github.com/annkennedy/bento/blob/master/docs/tracking_demo.gif?raw=true'> </div>Installation
The easiest way to keep your local version up to date is to clone this git repository. To launch Bento, enter addpath(genpath('path\to\bento\repository')) in the Matlab command line, followed by bento.
Bento requires the following software:
- Matlab 2014b or later
- Microsoft Excel (for assembling of metadata. This requirement will be softened in the future.)
You may also wish to install:
- Piotr's Matlab Toolbox if you use *.seq format videos
- Source2D Toolbox (in ca_source_extraction) if you use calcium traces extracted with CNMF_E
- JSONLab if you use our mouse tracker, MARS, and your MATLAB doesn't have native *.json support (pre-2017)
Citation
If you use Bento for your research, please cite:
Segalin, Cristina, Jalani Williams, Tomomi Karigo, May Hui, Moriel Zelikowsky, Jennifer J. Sun, Pietro Perona, David J. Anderson, and Ann Kennedy. "The Mouse Action Recognition System (MARS) software pipeline for automated analysis of social behaviors in mice." Elife 10 (2021): e63720.
Code Contributors
Bento was created by Ann Kennedy, but has benefitted from the suggestions of several members of the David J Anderson lab at Caltech, including Tomomi Karigo, Bin Yang, and Jalani Williams.
MARS, a pose estimation and behavior classification system that can be integrated with Bento, was created by Cristina Segalin, Jalani Williams, and Ann Kennedy, with support of members of the Anderson and Perona labs at Caltech. Code and documentation for MARS is coming soon.
Bento is an actively developed package, and we welcome community involvement. For questions about Bento, consult the project Wiki.
If you wish to contribute to Bento, or your question was not answered by the Wiki, please contact <A HREF="mailto:ann.kennedy@northwestern.edu">ann.kennedy@northwestern.edu</A>.
<br> <p><img src='https://github.com/annkennedy/bento/blob/master/docs/panels_demo.gif?raw=true' width='48%'> <img src='https://github.com/annkennedy/bento/blob/master/docs/PCA_demo.gif?raw=true' width='48%'></p>Licensing
Bento is licensed through Caltech; redistribution and use for academic and other non-commercial purposes, with or without modification, are permitted provided that conditions of the license are met.
