cortex-lab / cortex-lab/phy

Issue loading and visualizing previously curated data

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area: data status: needs-info type: bug
Dominant language
Python
Stars
430
Forks
187
Avg merge
2h 31m
Merged PRs (30d)
2

Description

I'm having an issue visualizing previously curated data in Phy2 after it has been moved to a server for backup. My intention is to review the manual curation of a previously curated recording (sorted using kilosort 2.5), but after copying the experiment folder from the server to my local drive (and changing the temp_wh.dat path in params.py), I'm unable to reload the manually assigned labels and the waveforms of almost all (but not all) of the 'neurons' look like electrical noise. The cluster_group.tsv file still has all the information regarding manual assignment, and I believe that all the phy2 output files are in the folder in the appropriate place. I am still able to reload and visualize manual curation for experiment folders that I haven't yet moved, but not ones that have been backed up to our experimental data server.

I've included a screenshot of what a lot of the noise looks like
Phy2_issue

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First steps

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  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with params.py and compare an experiment folder that still reloads correctly with one copied from the server. Check the temp_wh.dat path and the presence and contents of cluster_group.tsv and the other Phy2 output files. Done means manual labels reload and the neuron waveforms are no longer mostly electrical noise.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data-visualization
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Quiet
Clarity
Needs clarification
Newbie friendliness
38/100

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