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open-ephys / analysis-tools

Archived code for reading data saved by the Open Ephys GUI
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Binary dat files to Plexon Offline sorter #102

Open guilhemibos opened 1 year ago

guilhemibos commented 1 year ago

Hi

I'd like to try sorting the data with Plexon Offline sorter I acquired as binary files in OpenEphys. There is this old issue open: https://github.com/open-ephys/GUI/issues/146

It's pretty old, and I think there have been some big changes in OE and analytic tools. Is there something new on this? Anyone aware of how to do this?

Thanks Guilhem

jsiegle commented 1 year ago

I would recommend checking out Neo...it's been updated to support the latest OE Binary format, and I assume the PlexonIO class is compatible with Offline Sorter. But you'll have to test it and see.

guilhemibos commented 1 year ago

great I'll take a look!

ShaynDoe commented 1 year ago

@guilhemibos @jsiegle Hello, are you aware of a good way to use Plexon Offline Sorter with the OpenEphys binary data now?

jsiegle commented 1 year ago

I believe it's possible to load the .dat files (sometimes called .bin files) directly into Offline Sorter, but I haven't actually tried this myself. Does the Offline Sorter documentation mention anything about this? Note that this would just be the raw continuous data, and not the detected spikes (which are stored as .npy files).

ShaynDoe commented 1 year ago

Hello Josh, unfortunately though the Offline Sorter manual mentions being able to load continuous data, there isn't enough details or explanations on the best ways to deal with this. Are you aware of other resources used by the Open Ephys community for spike sorting, or if this has been discussed in other threads?

guilhemibos commented 1 year ago

I gave up trying to use Plexon's offline sorter, it does not seem adapted. Instead, I'm using Kilosort 2 (best for the type of probes I use than KS3). If I had to try again Plexon OS, I would split my continuous.dat file in as many channels that I have and try with that...

ShaynDoe commented 1 year ago

For anyone interested, I kinda found a cheat to make this work - I start with picking only the 4 channels for each tetrode from the OpenEphys continuous .dat files, and saving their timeseries as a .mat file. I then load it into the Plexon Offline Sorter (OS), and export it as a new .plx file. Then load this .plx file into OS again, and under the 'channels map', choose tetrode instead of single - these 4 channels are then saved as one tetrode and can then be sorted as needed.