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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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Loading Axion Biosystems AXIS data #1293

Open alexmascension opened 1 year ago

alexmascension commented 1 year ago

Hi!

Does spikeinterface support loading .raw or .spk formats of AXIS data? I don't see it in the docs, so I guess this format is not implemented.

Thanks!

JuliaSprenger commented 1 year ago

Hi @alexmascension Neo does not support this format as far as I can see. Feel free to open a PR to add a corresponding IO to Neo, see the instructions for adding a new format. As far as I know spikeinterface does not use Neo to load spiking data, so for the .spk files you will need to check with that project directly.

alexmascension commented 1 year ago

Hi @JuliaSprenger, I'm using the SpikeInterface module to do the loading, so I'm not sure if I'd be able to do the PR. I was redirected by @alejoe91 to open the issue here.

alejoe91 commented 1 year ago

@alexmascension do you know if there is a Python API to open Axion data?

alexmascension commented 1 year ago

I can't find it. They currently work with MATLAB files to load the data. I will try to contact them to see if they have some Python code for that (although I guess they won't).

samuelgarcia commented 1 month ago

In my lab someone have also this system. Apparently the raw is a standard binary file, so you must specify manually the number of channel the sampling rate et the dtype. In my case it was dtype=int16 8*64=512channels and sampling_rate = 12.5kHz. I did not find any header in txt, json or xml format along sie the raw file. I need to check with my colleague.

alexmascension commented 1 week ago

I ended up creating some scripts that do the job (you can find them here), although I guess that a better implementation can be done.