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Missing channels in phy

See original GitHub issue

Hi

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

waveforms

Issue Analytics

  • State:closed
  • Created a year ago
  • Comments:10 (5 by maintainers)

github_iconTop GitHub Comments

1reaction
mfvdcommented, Mar 25, 2022

Sorry, stupid error on my part. Forgot the sort the dataframe… It does make sense.

shank_ids_sorted

0reactions
alejoe91commented, Mar 25, 2022

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?

Read more comments on GitHub >

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