May 08, 2026
Behavior - Rotarod with Photometry
Forked from a private protocol
- Andrew Miller-Hansen1
- 1UCSF
Protocol Citation: Andrew Miller-Hansen 2026. Behavior - Rotarod with Photometry. protocols.io https://dx.doi.org/10.17504/protocols.io.81wgbjbzovpk/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: April 27, 2026
Last Modified: May 08, 2026
Protocol Integer ID: 315833
Keywords: vivo fiber photometry data during rotarod behavior, vivo fiber photometry data, rotarod with photometry, rotarod behavior, photometry, rotarod
Funders Acknowledgements:
Aligning Science Against Parkinson's
Grant ID: ASAP-020529
Disclaimer
*This protocol is adapted from what AJ did when he ran the first photorod experiments.
Abstract
This protocol describes collecting in vivo fiber photometry data during rotarod behavior
Before start
**Make sure to only use only lane three with the electrical tape on the rod for 'hard mode.'**
Set up
Turn on the following:
- Red light lamp
- IR lights (one above, one in front)
- iCon (camera controller)
- Computer, open up Synapse software
- Rotarod (switch on back right)
Click on Set Up logo to set up rotarod parameters:
- Select Ramp
- Set initial speed to 4 RPM
- Set final speed to 40 RPM
- Set ramp to 300 seconds
Return to Main Menu (four square logo at the top center)
In Synapse, go to “Preview” to check the camera view.
Try to match the camera view to this image.
Check the TTL for Trial start and fall (lane 3 drops) on Synapse by starting the rotarod and manually triggering lane 3 to drop.
Rotarod with photometry procedure
Click on the Start logo on the rotarod
Connect photometry cables to the mouse and preview to make sure signal looks fine on Synapse.
Gently place mouse on the rod facing towards the mirror (away from you) so that they would be walking forward in the direction of the rod rotation.
Before starting rotarod, check the following:
- Metal plate underneath the mouse is elevated
- Make sure there’s ‘slack’ on the photometry cables so that the mouse can fall without any hindrance or drag.
Start photometry recording on Synapse and let it run for ~30s of baseline.
At ~30 seconds, press “Run” on the rotarod then immediately after, press “Start” to start the trial. A TTL tick will show up to indicate the 'Start' of the trial.
Watch the mouse’s performance
When the mouse falls, make sure it triggers the metal plate to drop (that’s the TTL for fall). If it doesn’t trigger the drop, you should manually trigger it
Make sure the mouse falls ‘correctly.’ Don’t let it hang on to the rod and rotate around with the rod, Don’t let it stick it’s limbs out on the sides to slow the fall. Make sure the patch cable isn’t slowing down the fall.
Don’t block the light behind you too much when watching the mouse
After the fall, keep the photometry recording running for another ~40s before stopping the recording.
While waiting, visually inspect the rod to make sure they didn’t pee on the rod. If they did, wipe it dry with a kimwipe so that the wet/slipperiness won’t affect their next trial.
Start photometry recording while the mouse is on the bottom metal plate and let it run for 1-2 minutes.
Repeat steps 3 – 8 for an additional 7 trials (for a total of 8 rotarod and 8 bottom rest trials).
Clean up
Don’t need to do a full clean up between trials if the same animal is going back in the same lane, but always check to make sure the rod is dry of pee/poop so it doesn’t affect their next trial. If you plan on putting a different animal in the same lane, do a full clean up!
Remove the metal plate from the lane and use kimwipe to wipe away any poop and pee that has accumulated over.
Spray 70% ethanol on the metal plate and wipe clean.
Return metal plates to its original lane and make sure it “clicks” in so that it can lift up and drop down.
Spray 70% ethanol on paper towels and fully clean the rod and the barriers separating the lanes. (Hot tip, set rotarod to 40 RPM in constant mode to speed up cleaning)
Let air dry for a couple minutes before starting next set of animals.