IBL Average Trial

Installation

cd source_dir
git clone https://github.com/int-brain-lab/ibl-avg-trial-viz.git

The cloned directory contains usage examples and the main event_avgs.py file that can be imported with

from ibl-avg-trial-viz.event_avgs import *.

Must be used with the IBL’s iblenv

Usage

See the API reference for more detailed function documentation and examples.

examples/event_avgs_full_runs.py will run the pipeline on all insertions in the brainwide map and output event averages for raw spikes, baselined spikes, baselined and normalized spikes, and fano factor. The script also contains the (untested) code to generate the average raw spikes timelocked to different events. At the top of this

examples/event_avgs_testing.ipynb contains visualizations of output data including baseline normalized event averaged spike rates for clusters in different regions:

TODOs

• [ ] Import load_trials_df from brainbox.io.one instead of updated_one.py once (#492) is fixed. Delete updated_one.py

• [ ] Replace filter_eids.py system with Mayo’s updated one.alyx.rest query in get_bwm_sessions that only pulls insertions with the needed files. This will mean we won’t have to download everything when searching for good eids/pids.

• [ ] Fix file paths and plots in event_avgs_full_runs.py and event_avgs_testing.ipynb that were broken by recent updates to the event averaging pipeline.