catalystneuro / tye-lab-to-nwb

NWB Conversion project for the Tye lab at the Salk Institute.
MIT License
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Update fiber photometry pipeline #35

Closed weiglszonja closed 11 months ago

weiglszonja commented 11 months ago

Fix #37 to work in updated neuroconv environment resolve #25 by pinning ndx-photometry==0.2.0

weiglszonja commented 11 months ago

Usage example

conda activate tye_lab_to_nwb
pip install -r src/tye_lab_to_nwb/fiber_photometry/requirements.txt
python src/tye_lab_to_nwb/fiber_photometry/convert_session.py

or parallel convert with a session_config.xlsx file as described in fiber_photometry_notes.md

conda activate tye_lab_to_nwb
pip install -r src/tye_lab_to_nwb/fiber_photometry/requirements.txt
python src/tye_lab_to_nwb/fiber_photometry/convert_all_sessions.py
CodyCBakerPhD commented 11 months ago

As mentioned, will need to add a precise commit pin within the neuroconv branch https://github.com/catalystneuro/neuroconv/pull/579 to avoid issues with our new minimal requirement of hdmf>=3.10.0: I recommend 36fe8ba02c036e715a915ee66079391a50536fb2