Jun 23, 2026
Rearing Collection and Processing Protocol
- Kaitlin Southern1,
- Kyle Allen1
- 1University of Florida
- OrthoBME Lab Rodent Behavior Protocols
Protocol Citation: Kaitlin Southern, Kyle Allen 2026. Rearing Collection and Processing Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.kxygxre6kg8j/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: June 22, 2026
Last Modified: June 23, 2026
Protocol Integer ID: 319608
Keywords: rearing, preclinical models, behavior in rodent, cage cleaning, rodent, using acrylic cage chamber, rat, acrylic cage chamber, dataq acquisition system, rearing collection, precise rearing count, rearing behavior, processing protocol, experimental cohort, processing protocol this protocol detail
Funders Acknowledgements:
National Institute of Health
Grant ID: UC2AR082196
Abstract
This protocol details a standardized procedure for collecting rearing behavior in rodents using acrylic cage chambers coupled to a DataQ acquisition system. The workflow encompasses cage cleaning, and 10‑30‑minute recording sessions per rat, captured via DataQ software. Expected outcomes include high‑resolution voltage traces that translate into precise rearing counts and overall activity duration, enabling statistically robust comparisons across experimental cohorts.
Materials
1. Peroxigard
2. Paper Towels
3. Gloves
4. Gown
5. Rearing Chambers
6. Power Source
7. Data Acquisition Unit
8. Wires for connections
9. Computer
Safety warnings
NOTE: Before data is collected, animals should NOT be acclimated to the rearing cages. To avoid training effects, animals are not habituated before testing.
NOTE: Do not use ethanol to clean the acrylic or metal pieces as it will destroy it.
Ethics statement
These methods have been approved by the University of Florida Institutional Animal Care and Use Committee (IACUC).
Cleaning the Rearing Cages
Spray Peroxigard on paper towel and wipe the gait arena floor to remove debris.
NOTE: Do not use ethanol to clean the acrylic or metal pieces as it will destroy it.
Dispose of soiled towels in trash can.
Rearing Monitor Set Up
Place the rearing cages on a rack, just so they are elevated from the floor. Special lighting for this behavioral assay is not needed.
Open the DataQ Hardware Manager Software on the computer.
Ensure the DataQ Acquisition unit is plugged into the computer through USB.
Note: Tape wires down to the floor to avoid tripping hazards.
Rearing Device Wiring Set Up
Place each cylindrical acrylic cage on top of the small acrylic bottom piece.
Note: Ensure the circular metal portion of the bottom piece lines up with the bottom circular portion of the cage.
Connect the wires as shown in the figure.
Redirect all cage wires to corresponding individual channels on the DATAQ data acquisition unit.
Ground the device by connecting the negative (-) terminal on any of the digital ports (D0-D6) to an Earth ground.
Continue to the Sanity Check to ensure the setup is correct.
Sanity Check
Open the DATAQ Hardware Manager.
Allow 15 seconds for the device to appear on the DATAQ Hardware Manager.
Select the Model DI-2108 device.
Click ‘Start Windaq Software’.
You should see four plots centered around 0 volts, corresponding to the four rearing chambers.
If they are not centered at 0V, select Edit > Engineering Unit Settings > Set OffSet > Desired Reading = 0V > Ok > Next> (completed for each chamber).
For each chamber, place one hand on the bottom metal plate and touch the side panels with the other hand.
A voltage change signal should appear on the DataQ software.
NOTE: If there is no signal, the wire setup is likely inaccurate.
Troubleshooting: If the signal is too small to read, wipe the metal pieces with water to provide moisture. The moisture should amplify the output signal.
Data Collection
Grab the cages from the animal room.
Acclimate animals to room for 30 minutes in their cages before beginning.
If you have not done so already, open the DataQ Hardware Manager software on the computer.
Select the device name.
Select ‘Start Windaq’.
Place the rat in the activity monitor cage.
NOTE: Four rats can be recorded at one time. Be sure to record the chamber number corresponding to each rat.
Click File > Record.
Create a folder named RearingMonitoring_StudyName_Date on your external hard drive.
Name the file corresponding to the rats in each chamber.
Suggested: For each rat, set up your notebook to record time placed in the rearing cage, and total time spent in the chamber. This information is critical. On a separate sheet, record rat number, trial number and file name.
Click Open.
The file size should remain 360 Kilobytes.
Set the Recording Time to your desired trial length in [hours:min:sec].
NOTE: 15 minutes is recommended.
Put one rat in each chamber.
Quickly after rats are in the chamber, click Ok.
The Status bar on the bottom panel should read “RECORD” (highlighted in black).
After the trial time has ended, the recording will automatically stop, and the software will save the recording with the preselected name and location.
NOTE: If the recording needs to be prematurely stopped for any reason Select File > Stop. Status bar will return to STBY (standby).
Remove rats from the cages.
After each trial of animals, reset the chambers to 0V. Clean the cages between cohorts.
Save all files/folder from the day on your external hard drive.
Rearing Data Export from WinDaq
If not already downloaded, download the WinDaq Software (version DI-148U)
https://www.dataq.com/resources/obsolete/products/di-148/
Open the WinDaq Waveform Browser.
Open the file you want to view/convert.
Go to File > Save as.
Choose .csv on the right panel.
Name your desired file.
Click Ok.
Another prompt will pop up. Make sure only ‘Relative Time’ is checked.
Nothing should be in the comment boxes.
In the Edit tab, select Compression at the bottom.
In the Compression data display, select □ Max.
Hit the Max button.
In the WinDaw Waveform Browser, with desired file open, go to File > Export as Excel.
Note: Make sure the “Entire File” is selected.
Press the “Play” button.
Save the Excel file with a unique name including the Study Name, Animal IDs, Test date/time.
Note: Save this is the folder you created during data collection (‘RearingMonitoring_StudyName_Date’).
Close the Excel file.
Open the next file/recording. File > Open.
Note: In the pop-up click “Proceed with no save”. The data was already saved in the first step.
Repeat this process for all file recordings.
Shut Down Procedures
Save folder for that day on computer to external hard drive.
Ensure Windaq files are saved, in case data needs to be exported/viewed in the future.
Unplug DataQ device from the computer.
Processing Data
Open the Rearing_processing MATLAB file.
Set Path and Current Folder to the location of you saved .csv files. Ensure the processing MATLAB file is also in the folder.
On line 4, add your .csv files, separated by commas.
Define your threshold in line 7.
Name you output excel file in line 11.
Click Run.
Save figures to file.