Bonsai workflows

[ederancz]

Hi @RoboDoig. There are 2 example workflows below.

In general, all workflows should have the following:

1. Some sort of lab-book / metadata (time/date, animal ID, various experiment parameters e.g. gain in open loop).
2. Save processed optical sensor signals as styrofoam ball position. If using 1 optical sensor, then cumulative forward travel of the animal (say in cm) and rotation (0-360 degrees). This will of course need to be calibrated. In the future, we may want to use 2 sensors and average them for the rotation measure.
3. Trigger and save from 1 camera. In the future, online deepLabCut analysis would be sweet and perhaps only record pupil diameter and position.
4. A homing function. Currently using a hall-effect sensor and a magnet and rotate the platform until we activate it.

Workflow 1. Closed loop Inputs: Target position, speed, max acceleration Outputs: motor command, styrofoam ball position, video For the future: follow arbitrary waveform as a positional command

Workflow 2. Open loop Inputs: optical sensor signal, gain (between optical sensor and motor movement)
Outputs: motor command, styrofoam ball position, video

Regarding motor command, we should discuss motion control fairly soon. It is a big field, and I am not well-versed in it.

[RoboDoig]

Hi @ederancz that's great, thanks!

I'll start building some templates based on those specs and then test once we have our hands on the new HARP boards.

Agreed re: motor command. Our working assumption is that we will be driving something similar to the stepper motor / driver setup in the current vestibular platform docs. The motor HARP board should be flexible enough to control a different driver, but would be good to know any further requirements.

@glopesdev

[RoboDoig]

Initial workflows done in bonsai-workflows branch. Need to implement proper proportional control + HARP timestamps for camera frames in next iteration.

[ederancz]

Some further feature requests. For shortcuts, it would be cool to be able to use either command keys or the ONIX breakout board buttons.

• Can we have the workflow running an not record? This would be useful for homing, setting up an experiment, BonVision, ONIX - then e.g. Shift-R "Run Protocol" to record (AND SHOW BIG RED LIGHT)

• Homing - e.g. Shift-H, disable cameras, disable proportional motor control, rotate motor CW slowly until Hall sensor signal is true

• Ability to disable or enable proportional motor control (e.g. Shift-M)

[RoboDoig]

Can I assume that this issue is superseded by #49 ? Is there anything mentioned in this issue that is missing from the more recent workflow specs?

[EleonoraAmbrad]

yes, this issue can be closed!

Can I assume that this issue is superseded by #49 ? Is there anything mentioned in this issue that is missing from the more recent workflow specs?

I think we can close this issue, thank you !