Hi everyone! I have behavioural videos with corresponding timestamps of trials. I would like to be able to manually select trials based on animals' behaviour. I am looking for an open-source alternative of the CinePlex Studio or a similar software. I am aware of DLC, but it cannot detect when the animal e.g. closes eyes.
Dear Dmitry Kobylkov ,
Recently developed methods for video analysis, especially models for pose estimation and behavior classification, are transforming behavioral quantification to be more precise, scalable, and reproducible in fields such as neuroscience and ethology.
https://elifesciences.org/articles/79305
Regards,
Shafagat
General-purpose options:
- ELAN: https://archive.mpi.nl/tla/elan - Designed for linguistic analysis but offers versatile tools for various video annotations, including manual scoring and behavioral tagging.
- VLC media player: https://www.videolan.org/ - Basic video player with annotation capabilities and plugin support for more advanced features.
- OpenShot Video Editor: https://www.openshot.org/download/ - Video editing software with annotation tools and frame-by-frame analysis.
Specifically designed for behavioral analysis:
- DeepLabCut: http://www.mackenziemathislab.org/deeplabcut - Powerful tool for pose estimation and behavior classification using machine learning. Requires training your own models, but excels in automating analysis.
- SLEAP: https://github.com/talmolab/sleap - Lightweight alternative to DeepLabCut, simpler to set up and train for specific behaviors.
- BORIS: https://github.com/olivierfriard/BORIS - Comprehensive platform for observer-based analysis, offering manual scoring, data export, and statistical analysis.
- EthosVision XT: https://www.ethosvision.com/ - Freely available version of commercial software, good for tracking and analysis of simple behaviors.
- FIJI (ImageJ): https://imagej.net/ij/ - Primarily image analysis software, but includes plugins for video analysis and manual scoring.
Choosing the right tool:
The best software for you depends on your specific needs. Consider factors like:
- Complexity of behavior: For simple behaviors, basic video players with annotation features might suffice. Complex behaviors may require advanced tracking or machine learning approaches.
- Level of automation: Do you need fully automated analysis with machine learning, or manual scoring with data export and analysis tools?
- Technical expertise: Some tools require programming knowledge, while others have user-friendly interfaces.
- Community and support: Choose software with active communities and documentation for troubleshooting and learning.
Additional resources:
- Open-source tools for behavioral video analysis: https://elifesciences.org/articles/79305
- List of open-source behavioral analysis software: https://twitter.com/BehavEcol
My colleagues used B.O.R.I.S. for similar purposes, may be it will be useful for you too. https://boris.readthedocs.io/en/latest/
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