AllenInstitute / AllenInstitute/np_codeocean
Upload split recordings
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@bjhardcastle is already working on this.
Since Jul 29, 2026.
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- Python
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Description
- rearrange folders before upload
- in
experiment1folder, make consecutiverecordingNfolders - normal behavior of deleting all but the largest
recordingfolder must be skipped
- in
- adjust timestamps / sync messages as necessary, to appear as if all recordings are from one session
- Needs a processing script prior to upload for recordings resumed after software restart:
- samples numbers and timestamps need to appear under the same global clock
- adjust sync_messages.txt, sample_numbers.npy, timestamps.npy, and potentially other files, based on time separation between recordings https://open-ephys.github.io/gui-docs/User-Manual/Recording-data/Binary-format.html
- separation between recordings could be found to nearest 1 ms from sync_messages.txt, but it should be possible to find it more precisely with barcodes and sync.h5 (using npc_ephys)- [ ]
- upload without sorting, if possible
- sorting job must be triggered with concatenate/split-segments parameter set to True (see https://github.com/AllenNeuralDynamics/spikesorting-trigger-capsule/blob/main/code/main.py)
- keep a record of "unobserved" intervals - ensure in npc_sessions they're detected from the raw or sorted asset and recorded in the units table correctly (add via
pynwb.misc.Units.add_unit(obs_intervals=...)and use withnwb.get_unit_spike_times()+nwb.get_unit_obs_intervals())
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