Record with Open Ephys¶

This guide covers running an MSW behaviour session alongside an Open Ephys electrophysiology recording, with the two datastreams aligned by TTL barcodes.

Install the ephys extra:

pip install "murineshiftwork[oe]"

MSW controls the Open Ephys GUI remotely over its HTTP API. The full command reference is on the msw oe page; this page is the end-to-end procedure.

Wiring¶

Route the MSW barcode BNC output into a spare digital input on the Open Ephys acquisition board so the ephys recording carries the same time anchors as the behaviour session. See Barcode Sync for the concept.

1. Start the ephys recording¶

Start Open Ephys as the session host so it owns the session container that MSW and any other systems write into.

# Standalone ephys, or...
msw oe record --subject mouse001 --session-extension pxi

# ...a parent acquisition container that behaviour will join
msw oe record --subject mouse001 \
    --acquisition-extension ephys_multi_behavior \
    --session-extension pxi

On record, the plugin puts the GUI into RECORD and captures probe metadata (probe count and channel/stream layout) live from the GUI's /api/processors endpoint. That metadata is written to a session metadata JSON and, when an acquisition_manifest.yaml is present, stamped into it under metadata.open_ephys.

Check the state at any time:

msw oe status      # -> IDLE / ACQUIRE / RECORD

2. Run the behaviour session, attached to the host¶

Point msw run at the running Open Ephys host with --host openephys. MSW attaches to the same session container and writes its behaviour acquisition inside it, so ephys and behaviour share one session folder.

msw run -s mouse001 -t sequence --host openephys
# override the host address if it is not the machine default:
msw run -s mouse001 -t sequence --host openephys:10.0.10.111

Throughout the session MSW emits TTL barcodes on its BNC output, which the ephys board records on the digital input wired in above.

3. Stop¶

Stop the behaviour session normally, then return the GUI to idle:

msw oe stop

4. Align offline¶

Decode the barcode edges recorded on the Open Ephys digital input and match them to the behaviour barcodes to put ephys samples and trials on one timeline. The procedure is described in Barcode Sync.