SpikeInterface / SpikeInterface/spikeinterface
non-rigid motion correction on 2hr NPX recording
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- Dominant language
- Python
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Description
Hi, I'm testing spikeinterface on concatenating chronic NPX 1.0 recordings on at least two days and then spike sort.
I'm trying to use the non-rigid method motion correction which has been running smoothly on my one day recordings - about 1-1.5hrs.
After concatenating two days' recordings, I have:
all concatenated ConcatenateSegmentRecording: 383 channels - 30.0kHz - 1 segments - 288,029,739 samples
9,600.99s (2.67 hours) - int16 dtype - 205.48 GiB
The detect and localize peaks step runs okay, but the python session is killed after:
detect and localize: 100%|██████████████████████████████| 9601/9601 [5:01:00<00:00, 1.88s/it]
Killed
I wonder if this is due to memory usage? I'm running the session on Ubuntu 22.04, 64GB RAM, 8 Cores Intel Xeon E5-2640, Nvidia Titan X.
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Research direction
Start with the non-rigid motion-correction path after the detect and localize peaks step, using the reported concatenated 2.67-hour NPX recording as the reproduction case. Monitor memory during the transition from peak detection to motion correction on Ubuntu 22.04. Done means determining whether resource exhaustion causes the session termination and documenting or addressing the failure.
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Assessment
- Tech stack
- python
- Domain
- data, performance
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100