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SpikeGLX improvement

Open samuelgarcia opened this issue 5 years ago • 3 comments

#896 have implemented spikeglx reader

But SpikeGLXRawIO still need improvement that should be done in conjonction with spikeglx team:

  • better t_start handling
  • fine alignement between stream
  • ensure that all version (probe generation) are ok
  • handle channel id with str rather global channel counting

samuelgarcia avatar Dec 16 '20 11:12 samuelgarcia

For more details, see also https://github.com/NeuralEnsemble/python-neo/pull/896/files#r530494618

Further todos:

  • [ ] improve channel selection to preserve memmap in all possible cases, see https://github.com/NeuralEnsemble/python-neo/pull/896/files#r530847483

JuliaSprenger avatar Dec 17 '20 09:12 JuliaSprenger

I see in spikeglxrawio.py that "better handling of channel location" is also on the list.

For Neuropixel 1.0 probes at least, locations and channel ids/labels, as well as properties like whether the probes had the hardware highpass enabled, can be parsed right out of the .meta files.

I have code here to do this, in case it is helpful: https://github.com/CSC-UW/sglxarray#imecmap-objects This ImecMap object is what you'd want the functionality from.

grahamfindlay avatar May 18 '22 22:05 grahamfindlay

@grahamfindlay : we decided to move the probe description in probeinterface. https://github.com/SpikeInterface/probeinterface/blob/main/probeinterface/io.py#L669

This todo is old and should be remove. Maybe you could check that the probeinterface code is equivalent to your code.

samuelgarcia avatar May 19 '22 08:05 samuelgarcia