Missing channels in phy
See original GitHub issueHi
When doing the manual curation in phy, the WaveformView is missing a number of channels (pic below). Curiously, the missing channels are not consistent between units and there doesn’t seem to be a discernible pattern.
Also, when checking the units in phy, it seems like the channel position might have changed. I suspect this might have happened only because phy displays high amplitude waveforms of a given unit in fairly distant channels (e.g. channels 30 and 22 in the pic).
I used the following code to define my probe to device map:
manufacturer = 'cambridgeneurotech'
probe_name = 'ASSY-37-Fb'
probe = pi.get_probe(manufacturer, probe_name)
# Match to device (RHD headstage) map. In this case it was manually corrected because probeinterface might be wrong.
device_channel_indices = [
29, 19, 10, 18, 28, 30, 20, 17, 21, 31, 22, 16, 23, 27, 26, 25, 24, 7, 6, 5,
4, 8, 9, 3, 11, 2, 12, 1, 13, 0, 14, 15]
# set channel ids based on manual probe map from cambridge site and RHD map.
probe.set_device_channel_indices(device_channel_indices)
# set recording channels to new probe>RHD map.
rec_probe = rec.set_probe(probe,
group_mode='by_shank')
and the following code to export to phy:
waveforms_ms4 = si.WaveformExtractor.create(rec_cashed,
sorted_ms4,
'waveforms',
remove_if_exists = True)
# set params
waveforms_ms4.set_params(ms_before = 2,
ms_after = 2,
max_spikes_per_unit = 1000,
return_scaled=True)
# run extractor to get waveforms
waveforms_ms4.run_extract_waveforms(n_jobs = -1,
chunk_size = 30000)
# export spikes to phy
export_to_phy(waveforms_ms4,
'./phy_ms4',
compute_pc_features = True,
compute_amplitudes = True,
progress_bar = True)
Any idea of what might have gone wrong? Cheers
Issue Analytics
- State:
- Created a year ago
- Comments:10 (5 by maintainers)
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Sorry, stupid error on my part. Forgot the sort the dataframe… It does make sense.
So you need to sort the probe dataframe by
device_channel_index
. Can you also show that column in the screenshot? Is it from 0 to N-1?