NeuralEnsemble / python-neo

Neo is a package for representing electrophysiology data in Python, together with support for reading a wide range of neurophysiology file formats

http://neo.readthedocs.io/en/latest/

BSD 3-Clause "New" or "Revised" License

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SpikeGLX improvement #923

Open samuelgarcia opened 3 years ago

samuelgarcia commented 3 years ago

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

JuliaSprenger commented 3 years ago

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

grahamfindlay commented 2 years ago

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.

samuelgarcia commented 2 years ago

@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.