Create module to make VBN NWB file

AllenInstitute / ecephys_etl_pipelines

Pipelines and modules for processing extracellular electrophysiology data

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Create module to make VBN NWB file #29

Closed wbwakeman closed 2 years ago

wbwakeman commented 2 years ago

Following the design of VBN Data Object in #9, we need to create a module that will use that to make an NWB file for a VBN session. This module will eventually be launched by a LIMS queue and run in a singularity container on a node of the on-prem compute cluster.

Tasks:

Implement the individual methods specified in the design
Create an input file that will be used during development of the module
Use the module to create the NWB file
Send an example output NWB file to Corbett for review
Address feedback

Validation criteria:

Module exists and code is merged to create the NWB file
Feedback is recorded and has been addressed

wbwakeman commented 2 years ago

Links to some useful NWB background information: https://training.incf.org/lesson/what-nwb-short-intro-nwb-enabled-tools https://training.incf.org/lesson/extracellular-electrophysiology-pynwb

And some ancient history, but there may be some useful information in there http://confluence.corp.alleninstitute.org/display/IT/NWB+version+history

wbwakeman commented 2 years ago

For specific questions about the NWB standard and implementation, feel free to contact: Ben Dichter: bdichter@lbl.gov Ryan Ly: rly@lbl.gov

ns706 commented 2 years ago

https://alleninstitute-brainscience.atlassian.net/wiki/spaces/ITP/pages/1003683841/AllenSDK+Data+Object+organization+for+VBN

ns706 commented 2 years ago

https://alleninstitute-my.sharepoint.com/:x:/g/personal/nathan_sjoquist_alleninstitute_org/EWQAQtWBmDhCiQipTSOPq3sBrWhpG67xgcL1MMuRrzP5uA?e=IFyZ4P&CID=061e5053-8f52-d3fb-3c61-8191e8b50adf

danielsf commented 2 years ago

Closing this in favor for AllenSDK ticket #2327 (which will encompass refactoring this code) and another ticket to be written to write the infrastructure to ingest these files and return EcephysSession objects (or some equivalent)