Open Field Workflow

[Aaron]

Hello Bonsai Users,

We created an Open Field Workflow from Bonsai.  There is also documentation provided on how the workflow operates. The goal was to provide a user experience similar to that of commercial tool. The workflow is ROI dependent, so it can adapted for other behavioral assays as well, such as Real Time Place Preference. We would love to hear any feedback, comments or questions on the workflow!!

Aaron

[Gonçalo Lopes]

Hi Aaron,

Thanks for posting this! It's a really lovely example of how to structure a complex nested workflow with configuration properties and an interactive dynamic interface. It will definitely give me a lot of food for thought in terms of thinking how to enable easier creation of rich user interfaces in Bonsai, which is something that is starting to make more and more sense.

One thing that might be helpful is to externalize all configurable properties to the top-level.

I've been thinking of providing an easier way to allow starting Bonsai with a minimalist skin for running experiments like this, which would simply open the properties window containing all top-level externalized properties (categorized) and a simple button to start the experiment along with any visualizers and interactions which have been defined by the program.

Basically this is a minimal UI with just the Properties panel and the visualizers and no workflow editing support. I believe that might simplify the information interface tremendously for experimenters. I've created an issue to keep track of this, so keep an eye out for it to any progress if you are interested: https://github.com/bonsai-rx/bonsai/issues/686

I'm also happy to help turn this example into a package for the Bonsai Gallery, so people can find and install it through there. Let me know if this would be interesting.

Nice work!

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[Aaron Norris]

Thank you for the feedback.

We are implementing this open field and a real-time place preference version and finding a few small bugs as we go. Would be great to make these into Gallery examples once I feel like we have it better tested, which we should in the next few weeks. Hopefully, they will be useful to other.

Two questions -

Was this "One thing that might be helpful is to externalize all configurable properties to the top-level." a suggestion for change in this workflow or more general comment?

Is there a was to link the frame rate of video writer to the frame rate of video capture? Example - video capture is set to 60 fps but video writer is still (perhaps mistakenly) left at 30 fps.

Thanks

Aaron

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[Vincent Prevosto]

Gonçalo, a minimal UI would be super useful !

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[Gonçalo Lopes]

Hi Aaron and Vincent,

I will try to get minimal UI to come out as a feature in Bonsai 2.6, which should hopefully be out by the end of September / October. I will write some examples of how to use it which should help to make it clear when and why to use externalized properties at the top-level.

Aaron, regarding linking the frame rate of capture to frame rate of writer, yes, it is possible by using a property source. However, I suspect that you would want to extract the frame rate dynamically from the video itself, which at the moment is not easy to do. I've been considering improving the capabilities of the FileCapture node (or adding a few new nodes) so it is possible to access the video metadata itself to make these kinds of decisions. I've raised an issue to keep track of this feature, so any development news would go there: https://github.com/bonsai-rx/bonsai/issues/700

Thanks,

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[harda...@gmail.com]

Hi all,

We are very interested in this UI as well, so if anyone has updates to these workflows please let us know. Goncalo, did a minimal UI for this come out with the latest release? Thank you all for curating these awesome resources.

best,

Andrew

[Gonçalo Lopes]

Hi Andrew,

Yes, the minimal UI did make it to the new Bonsai 2.6 but is still quite barebone and requires preparation to use.

If you launch Bonsai using the command-line option --no-editor and there is a .layout file with the visualizers to be used, then Bonsai will open all the visualizers and display them in the correct position but without starting the editor window. In this case, a tray icon with Bonsai will also be added which can be used to stop the workflow.

In practice, to launch a dedicated interface would probably require either a little script, or a shortcut to bonsai adding the --no-editor flag and also preparing the workflow beforehand with all the visualizers and editors (e.g. property grid) to be shown.

At some point we will put out a blog post or example of this.

Hope this helps.

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[Andrew Hardaway]

Hi Goncalo!

Thanks for the update. We will give it a try!

best,

Andrew

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J, Andrew Hardaway
Assistant Professor

Department of Psychiatry & Behavioral Neurobiology
University of Alabama at Birmingham School of Medicine

he/him/his