Guide/Pre-Experiment Checklist
Workflow
Overview
Complete this checklist at the start of every recording session, including sessions with animals you have recorded from before. The majority of session-level data loss comes from steps that were assumed rather than verified. This checklist takes less time than recovering from a failed session.
and is transcluded there for use during sessions. Complete it immediately before every recording session. See Guide/Data Acquisition for the full session
procedure.Before Mounting the Miniscope
| ☐ | Check |
|---|---|
| ☐ | Storage space: Confirm sufficient drive space for all data
streams expected this session — Miniscope video, behavioral camera video, and timestamp files. Calculate the expected file size before assuming space is available. |
| ☐ | Imaging sensor: Inspect the imaging sensor. Clean with lens
paper and appropriate solvent if dust or debris is visible. If the sensor was removed between sessions, reseat it in the same orientation as before and confirm it is fully secured. |
| ☐ | Reference snapshot: Confirm the reference snapshot for this
animal is accessible and open for comparison. |
| ☐ | DAQ software: Open the Miniscope DAQ application and confirm
the DAQ board is recognized. |
| ☐ | DAQ indicator lights: Confirm the three indicator lights on
the DAQ board are on. |
| ☐ | Write speed: Confirm the write speed of the recording drive
is sufficient for your target frame rate. A dropped-frames problem discovered after a session cannot be corrected. |
| ☐ | Behavioral camera: Confirm the behavioral camera is
connected, positioned correctly, and producing a clean live feed in your tracking or recording software. |
| ☐ | Commutator (if applicable): Confirm the commutator rotates
freely. Connect the Miniscope cable above the commutator and confirm the live image passes through cleanly. |
| ☐ | Humidity: Confirm relative humidity is above 40% in the
recording space. Adjust if needed and allow 10–15 minutes for the space to equilibrate before the session. |
| ☐ | Lighting: Confirm arena lighting is set to the same
configuration used in all prior sessions for this cohort. |
After Mounting, Before Starting Recording
| ☐ | Check |
|---|---|
| ☐ | Miniscope seating: Verify the Miniscope is flush against the
baseplate and not tilted. Confirm the set screw is tight and not obstructing the imaging path. |
| ☐ | Image quality: Compare the live image to the reference
snapshot. Blood vessel positions, brightness, and contrast should closely match. If they do not match, troubleshoot before proceeding. |
| ☐ | Mechanical stability: Gently move the Miniscope body while
watching the live image. Movement of the scope body should not cause movement of the brain image. If it does, the scope is not seated correctly. |
| ☐ | Cable management: Set cable slack so the animal has full
freedom of movement. Confirm the animal cannot reach and chew the cable. |
| ☐ | Animal behavior: Allow 1–2 minutes for the animal to settle
after mounting. Confirm behavior resembles the habituated state — active, exploratory, not freezing or pressing against walls. |
snapshot: Check (1) whether the Miniscope is fully seated against the baseplate, (2) whether the set screw is obstructing the optical path, (3) whether LED intensity or gain settings have changed from the saved values, and
(4) whether the baseplate has shifted since the last session.After the Session
| ☐ | Check |
|---|---|
| ☐ | Immediate data folder inspection: Open the data folder
immediately after the session ends. Confirm the expected files are present and non-zero in size before doing anything else. |
| ☐ | Behavioral camera data: Confirm the behavioral video file was
captured, is the expected duration, and is playable. |
| ☐ | Timestamp files: Confirm timestamp files are present and have
the expected number of entries. |
| ☐ | Session log: Complete the session log entry for this session
before the next session begins. |
| ☐ | Data backup: Back up all session data before the next
session. |
accidental deletion after a session that has not been backed up is unrecoverable. There is no post-hoc solution. Back up before doing anything
else.