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bonsai.miniscope's Introduction

NOTE: This library is now read-only. Development is now taking place on the OpenEphys.Bonsai.Miniscope repo.

Bonsai.Miniscope

Bonsai package for controlling and acquiring data from head-borne miniscopes for calcium imaging.

It contains the following nodes:

  • UCLAMiniscope: UCLA Miniscope V3 using legacy DAQ firmware. Use this if you have an old DAQ box and have not updated firmware recently.
  • UCLAMiniscopeV3: UCLA Miniscope V3 using updated DAQ box and firmware. Use this if you are also using the V4 scope.
  • UCLAMiniscopeV4: UCLA Miniscope V4 with integrated IMU.
    • NOTE On some V4 miniscopes, the IMU data will appear jumpy with some or all of the components taking the same value. This is a known issue, and has been addressed in later versions of the Miniscope hardware. See this issue for more information.

Feel free to submit an issue or PR if you want to add your Miniscope to this package.

This project was created and is maintained by Jonathan P. Newman. If you use it in your work, please reference this repository in any papers or presentations.

Upstream

This project is a fork of Bonsai.Vision.CameraCapture

License

MIT

bonsai.miniscope's People

Contributors

galenlynch avatar glopesdev avatar jbscherrer avatar jonnew avatar

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bonsai.miniscope's Issues

turn off LED when stopping a recording?

Ive just started playing with this package, so let me know if there is a more appropriate place to ask questions.

I'm wondering if there is a way to set the LED to 0 when I stop the bonsai recording? Its not a big deal to stop the recording, then restart and manually set the LED power, but it would be nice to have it potentially be automatic.

Thanks!

Add example workflows with online analysis features

It might be useful to have features present in Miniscope-DAQ-QT software (online df/f, ROIs, saturation, heading) for users that migrate from one to another and might expect the same functionality. Some may be part of the package, others part of the example workflows.

Add support for DAQ hardware I/O Input trigger

In the Miniscope DAQ-QT software, setting the input from low to high in the DAQ Input trigger I/O channel starts the recording and high to low stops the recording.

After acquisition is stopped, miniscope LED stays on in both Bonsai and Miniscope DAQ-QT. In the DAQ-QT soft triggerable mode, the scope LED is turned on and off.

External Trigger option

I'm trying to use this plugin inside Bonsai without depending on the Miniscope program.

It could be really helpful to have the option to turn on and off the "External Trigger" mode of the Miniscope, directly from the Miniscope node in Bonsai.

Specifically, I'm talking about the option to start and stop recording with Miniscope through an High/Low signal from an external trigger.

Compiler throws warning on compilation

warns that Bonsai.Design cannot be found:

C:\Program Files (x86)\MSBuild\14.0\bin\Microsoft.Common.CurrentVersion.targets(1820,5): warning MSB3245: Could not resolve this reference. Could not locate the assembly "Bonsai.Design". Check to make sure the assembly exists on disk. If this reference is required by your code, you may get compilation errors.

VS solution points to invalid project file

C:\Users\Galen\Documents\Code\Bonsai.Miniscope\UCLAMiniscope\Miniscope.csproj : error  : The project file could not be loaded. Could not find a part of the path 'C:\Users\Galen\Documents\Code\Bonsai.Miniscope\UCLAMiniscope\Miniscope.csproj'.  C:\Users\Galen\Documents\Code\Bonsai.Miniscope\UCLAMiniscope\Miniscope.csproj

Should be \Bonsai.Miniscope\Bonsai.Miniscope\ instead of Bonsai.Miniscope\UCLAMiniscope\

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