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Spike sorting curation
Julie Fabre edited this page Aug 2, 2023
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Phy is a gui for manually reviewing and modifying the results of the automatic algorithm. The template-gui has been developed for use with results produced by Kilosort.
See this documentation for a user-friendly guide to spike sorting Neuropixels data, and an example manual curation workflow.
Manual curation is inherently noisy and biased. Thankfully, most of manual curation can be automated with quality metrics, although we currently don't have any solutions to split or merge spikes automatically. Several toolboxes exist to compute these quality metrics:
- bombcell from the Carandini & Harris lab, in MATLAB. Adding an option to split and merge spikes is currently underway. See the wiki
- sortingQuality from Nick Steinmetz, in MATLAB
- ecephys_spike_sorting from the Allen Institute, in Python
- ibl brainbox metrics (under development) from the International Brain lab, in Python
- About Neuropixels and probe types
- Configurations and selecting electrodes
- Equipment List and example setup
- Probe handling/mounting
- Chronic implants
- Probe sharpening
- Probe care
- Planning probe trajectories
- Acquisition software
- Referencing and Grounding
- Gain settings
- Filter settings
- Impedance testing
- Synchronization
- Multiple probes on one computer
- Light artifacts
- Troubleshooting
- Recommended preprocessing
- Spike sorting
- Spike sorting curation
- Other analysis methods, and tutorial for getting started with Neuropixels Phase3 data in matlab
- Identifying tracks in histology