SpikeInterface / SpikeInterface/spikeinterface
Questions about unit conversion (ADC vs µV) in SpikeInterface + Kilosort4 pipeline
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Description
Hi,
I am working with extracellular recordings acquired using Intan and flexible electrodes. My current data processing pipeline is:
- Load raw
.rhddata recorded with Intan - Preprocess the data using SpikeInterface
- Save to binary format
- Run spike sorting with Kilosort4
- Use SpikeInterface quality metrics for initial labeling
- Manually curate and correct units in Phy
- Extract template waveforms using SpikeInterface
After loading the raw Intan data, is it sufficient to apply unsigned_to_signed() Handle unsigned data types to convert the data to signed integers? Do I need to apply both unsigned_to_signed() and scale_to_uV() Work with physical units in SpikeInterface recordings , or is using unsigned_to_signed() alone sufficient before preprocessing and spike sorting?
If I don’t convert the data to microvolts (µV) during preprocessing and keep everything in raw ADC units, will this affect:
- Kilosort4 spike sorting results?
- SpikeInterface quality metrics?
- Template computation?
- Any downstream analyses?
My understanding is that most spike sorters (including Kilosort) operate on raw ADC units, but I would appreciate clarification on best practices in this case.
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Research direction
Start with the linked SpikeInterface documentation on unsigned data and physical units, then trace the Intan loading, binary export, Kilosort4, and quality-metrics steps described in the issue. Clarify which unit conversions are expected at each stage and document the effects on sorting, metrics, templates, and downstream analyses.
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Assessment
- Tech stack
- python
- Domain
- data, machine-learning
- Issue type
- Documentation
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100