Comments (7)
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.
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great I'll take a look!
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@guilhemibos @jsiegle Hello, are you aware of a good way to use Plexon Offline Sorter with the OpenEphys binary data now?
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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).
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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?
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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...
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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.
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Related Issues (20)
- Splitting and Merging .dat Files HOT 3
- Trouble loading events data in matlab when saving in flat binary format with the updated GUI: load_open_ephys_binary.m looks for channels.npy HOT 3
- Failing to read metadata.npy for TTL events in this specific setup HOT 4
- Converting continuous.dat into SpikeGLX flat binary HOT 4
- data and timestamp length unequal using load_open_ephys_binary HOT 4
- Session? HOT 1
- Flat binary file has more/less samples than expected HOT 4
- How to convert .continuous format to flat binary for using in Klusta HOT 1
- How to display the specific time point for spikes ? HOT 1
- load_open_ephys_data_faster.m memory error HOT 5
- Import continuous data recorded by neuropixels HOT 11
- Opening the binary data HOT 4
- issue running TT openephys data recorded in binary to Mclust
- Using analysis tools in Jupyter Notebook HOT 4
- Merging multiple OpenEphys binary (continuous.dat) files HOT 1
- Info Channel Header Location HOT 2
- Missing Probeinterface file for Neuropixel 1.0 (Open Ephys)
- recovering timestamps HOT 1
- OEP v0.6.2 Python KeyError: 'source_processor_sub_idx HOT 3
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