allenneuraldynamics / aind.behavior.bcinomovement

A repository for the aind-bci-no-movement experiment

aind-bci-no-movement

• aind-bci-no-movement
  • Deployment
  • Prerequisites
  • Notes on data-schema regeneration

Deployment

To deploy the Bonsai code, run ./bonsai/setup.cmd. This small script will download and regenerate the current bonsai environment (see tutorial for further details.)

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Prerequisites

These should only need to be installed once on a fresh new system, and are not required if simply refreshing the install or deploying to a new folder.

• Windows 10 or 11
• Visual Studio Code (highly recommended for editing code scripts and git commits)
• Git for Windows (highly recommended for cloning and manipulating this repository)
• .NET Framework 4.7.2 Developer Pack (required for intellisense when editing code scripts)
• Visual C++ Redistributable for Visual Studio 2012 (native dependency for OpenCV)
• FTDI CDM Driver 2.12.28 (serial port drivers for HARP devices)
• Spinnaker SDK 1.29.0.5 (device drivers for FLIR cameras)
  • On FLIR website: Download > archive > 1.29.0.5 > SpinnakerSDK_FULL_1.29.0.5_x64.exe
• NI-DAQmx 19.0 (drivers for NI-DAQ devices)

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Notes on data-schema regeneration

1 - Install bonsai.sgen dotnet tool

2 - Run bonsai.sgen targeting the root schema in src/DataSchemas. E.g.:

To regenerate the loggers, use:

bonsai.sgen --schema "src\DataSchemas\bci-no-movement-logging.json" --namespace BciNoMovement.Logging --root BciNoMovementLogging --output "src\Extensions\BciNoMovementLogging.cs" --serializer NewtonsoftJson YamlDotNet
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aind.behavior.bcinomovement's Issues

Camera Lag

The longer a session runs, the slower the camera acquisition seems to be.

LoadCell_Offset Not Effecting Load Cell Readout

There may be an issue with how the load cell is reading movement. To summarize, when lightly tapping upwards on the mouse chair, large spikes are visible in the raw data (indicated as "up" in plot), however, tapping down with similar pressure only shows barely noticeable deflections in the load cell data (indicated as "down" in plot).

The command that sets the load cell bias:

operation=Operation(loadCellOffset=[50, 0, 0, 0, 0, 0, 0, 0], loadCellIndex=0)

also does not seem to affect the readout of the load cell. All channels and several values ranging from -127 to 127 have been tried, none have had an effect on this phenomenon.

Implement new harp manipulator

Refactor visualizers to new bonsai gui package

Plot Adjustments

For plots in general, can we add axis labels?

Also, for movement (and BCI) plot, can we adjust the axes of each plot to show a fixed time window (x) and adjust the y axis to be 0-1000 for the movement plot?

Might be separate discussion on whether it makes sense to do this for the motor position plot, because it is useful to see motor movement for the entire session on this plot. It offers a good way to count the number of trials that have occurred. The only drawback is that as the session gets longer, there is lag time the comes up when updating the plots, it seems.