Use electrode site layout information for spike sorting and/or visualization

vandermeerlab / data-formats

Playing around with different data formats and loaders

MIT License

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Use electrode site layout information for spike sorting and/or visualization #12

Open mvdm opened 4 years ago

mvdm commented 4 years ago

Both #5 and #11 would benefit from having probe geometry included.

This information should be part of a promoted data set, but isn't currently included. It requires:

Neuronexus Site Map which relates probe sites to pins on probe connector
Neuralynx channel mapping which relates pins to AD channels
Specific file information for a given session relating AD channels to .ncs files

Initial milestones would be:

[ ] Make a geometry file for an example tetrode session
[x] Make a geometry file for an example 32ch probe session

mvdm commented 4 years ago

We discussed this and converged on the idea of defining this mapping in terms of Neuralynx AD channels (not filenames). A given Neuralynx AD channel corresponds to a specific pin on the animal side of a given headstage. So as long as experimenter plugs in this headstage in a consistent orientation, a given AD channel will map onto a specific probe site (x, y coordinates). Neo extracts the AD channels from the .ncs headers, so can use these going forward.

manimoh commented 3 years ago

Probe file for 32 channel probe (NeuroNexus A4x2tet)

mvdm commented 3 years ago

does it make a difference at some point, like in the manual touch-up viewer stage?

manimoh commented 3 years ago

does it make a difference at some point, like in the manual touch-up viewer stage?

The manual curation using phy is the only place where the channel layout is used (for visualization). I had previously added locations manually instead of using the probe file, so it didn't make a difference in this case.