SpikeInterface / SpikeInterface/spikeinterface
Plot_unit_locations error?
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Description
Hi,
I have a recording on neuropixel 2.0 using openephys and performed sorting on kilosort 4 (outside of spikeinterface). I then loaded both the recording and sorting into spikeinterface to create a sorting_analyzer object. After computing random spikes, templates, spike and unit locations, I tried plot_unit_locations which gave a plot where most of the units seemed to be on the rightmost shank, while there are also many units on the third from left shank, where there aren't even recording channels selected. Finally, some units are plotted in between shanks. These locations do not match the spike locations visualization from kilosort either.
Plot_unit_locations output:
I plotted the spike_positions.npy file from kilosort 4:
To look at a single unit in detail, here is unit 52 highlighted in red on the second from left shank (for ease of viewing I did not plot all the spikes from other units). The plot_unit_locations widget however highlights unit 52 on the 4th shank, at a different depth as well.
May I know if I am doing something wrong?
This is my code:
recording = si.read_openephys(recording_file_path)
kilosort_results = si.read_kilosort(kilosort_file_path)
analyzer = si.create_sorting_analyzer(sorting=kilosort_results, recording=recording,format="binary_folder",return_scaled=True, folder='my_save_path')
si.compute_random_spikes(analyzer)
si.compute_templates(analyzer)
si.compute_spike_locations(analyzer)
si.compute_unit_locations(analyzer)
si.plot_unit_locations(analyzer,backend='ipywidgets')
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Research direction
Start with the provided read_openephys/read_kilosort workflow and the compute_spike_locations, compute_unit_locations, and plot_unit_locations entry points. Compare their coordinates with Kilosort 4's spike_positions.npy, reproducing the discrepancy for unit 52. Done means the plotted units match the expected shanks and depths, or the coordinate mismatch is clearly identified.
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Assessment
- Tech stack
- python
- Domain
- data-visualization
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100