Manual curation of event length in videos? [solved]


I am looking for a plugin (or maybe in-built?) that can help me curate the length of behavior in a running video.

I have a scratching behavior that I can see in the video that I want to quantify (start, end, length). This behavior happens rather often so using a timer is tedious.

Does a plugin exist where the video is running and I click one button for start of behavior and another for the end of behavior (and that repeated for every cycle the behavior happens)?

thanks in advance!


As for your options… you could think about creating your own script in Fiji. Using Script Parameters, you can make a user-interactive script that ‘might’ be able to achieve what you want (printing time stamps for ‘start’ and ‘finish’ from manual clicks, calculate time difference, print out results, etc.). Here are some helpful links to get you started:

You could also take a look at DeepLabCut. By providing a bit more information on your datasets and image analysis question - @AlexanderMathis / @MWMathis should be able to guide you a bit better as to whether or not DLC is the correct tool to apply.

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You can use DeepLabCut to automate movement analysis, then use simple metrics to determine stat, stop, etc (some post-DLC tools we provide currently are on DLCUtils). or if you just want a manual annotation tool, I would check out BORIS


Thank you @etadobson for your quick response, learning scripting with Fiji is on my to-do list for a while, maybe it is the final push to give it priority!

Thank you for pinging @MWMathis, too!

I have used DLC to do simple tracking of animals in a cage from above and also thought about using it for this particular case. However, the behavior I am trying to track is the lifting of a paw and then scratching on the back. As the videos I am acquiring are all from above, this might not be so trivial. And adding a sideways view for a “3D” analysis it a little overkill.

However, BORIS looks like just the option for my current needs, so thanks a lot for mentioning it!