Marigold
Zebrafish pose tracking made easier
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Step 1
Label data
Extract representative images from your behavioral recordings and label them with animal pose coordinates.
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Step 2
Train model
Use your labeled data to train a neural network custom-tailored for animal pose tracking with your unique experimental setup.
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Step 3
Analyze behavior
Sit back and let your trained model churn through new behavioral recordings, then export the generated data and visualizations.
Learn more
What is Marigold?
Marigold is a free and open source web app for analyzing zebrafish behavior. It is being developed by Gregory Teicher (gteicher at umass dot edu) in the Downes Laboratory at University of Massachusetts Amherst.
Marigold is compatible with a wide range of experimental paradigms, particularly at embryonic and larval stages. As long as each region of interest only contains a single fish, it is likely that Marigold can track it.
Check out our paper in BMC Bioinformatics for more info! (And please consider citing the paper if you find Marigold useful!)
Marigold is licensed under the GNU General Public License version 3 (GPLv3) or later. You can view its source code on GitHub.
Currently, Marigold should be regarded as alpha-level software. That means it is still missing elements of the planned functionality, contains some known bugs, and is likely to also contain unknown bugs. Additionally, it may not be compatible with future versions of itself. Nevertheless, since we've found Marigold useful even in its current state and hope you will too, we've released it as-is while we continue to work on it. In the meantime, please check out the GitHub repository to find out more about currently known issues and planned improvements.
You are using Marigold version: v0.0.0-alpha-12.