Capture high frame rate videos of a custom-made, CatWalk like setup for mice using a FLIR's BlackFly camera. A video is saved to disk every time motion is detected and while locomotion satisfies the criteria defined in the configuration.
See related resources:
- Install Spinnaker SDK
- Install Python version 3.8 (notice that the only supported Python version is 3.8).
- Open
cmd - Run
pip install walkwayorpython -m pip install walkway.
- Power on IR light source.
- Plug in camera to computer.
- Adjust camera settings using SpinView (optional)
- Adjust camera aperture and focus to view region of interest under the light conditions expected during the experiment.
- Adjust image format to limit the view to the apparatus' walkway. Note that some parameters can only be changed when acquisition is off.
- Open
cmd - Run
python -m walkway.captureto start auto-triggering. - Press
qon the GUI orctrl+con the command window when done. - Video files are saved to cmd's working directory (defaults to
C:/Users/<your username>in Windows). You maycdto a different directory prior to start capturing to save videos elsewhere. - You may use a configuration file in JSON format with
python -m walkway.capture --configuration configuration.json; this will override any parameters previously set to the camera. - Run
python -m walkway.capture --helpfor more information. - Run
python -m walkway.guito open a GUI with a single camera. - Run
python -m walkway.experimentto open an experiment with two FLIR cameras and a Petteron microphone.
MATLAB scripts to analyze data collected with the Walkway setup.
See related resources:
- MATLAB (last tested with R2023a)
- Install MATLAB
- Download and extract these scripts to Documents/MATLAB folder.
To export a table with gait metrics:
- Create a new data loader to match your DLC data columns (use
loadData.mas a reference). - Edit
process.maccording to your experimental setup and run.
For further analysis, such as replicating those described in the paper paper, also modify paper.m and preprocess.m.
Make sure to run startup.m every time you restart MATLAB to add dependencies to MATLAB's search path.
- For the data loader associated to the paper, DLC files are expeected to be saved in the following format:
[Sex][GroupId][MouseId]-[Mode][Year][Month][Day][Hour][Minute][Second][Microsecond]For example:F0203-T20220124110229988302Sex: 1 character encoding sex: M or F GroupId: 2-digit number (e.g. 01) MouseId: 2-digit number (e.g. 02). Mode: 1 character encoding recording mode, T: automatic trigger, C: manual trigger. Year: 4-digit number (e.g. 2023) Month, Day, Hour, Minute, Second: 2-digit number. Microsecond: 6-digit number.
For group testing, where multiple animals may trigger detection, MouseId can be omitted from the filename:
M02-C20220128162425752937
CAD files and assembly instructions for a Walkway apparatus.
See related resources:
- 6mm clear acrylic sheets
- Strip of IR LEDs
- Power supply
- Female DC barrel jack adapter
- Power cord
- BFS-U3-16S2M-CS USB Blackfly® S, Monochrome Camera
- USB 3.1, Type-A to Micro-B
- Varifocal lens (Fujinon DV3.4X3.8SA-1)
- Laser cut the acrylic sheets using the provided CAD drawings. Remove protective film.
- Use 2 part epoxy to place the LED strips facing up as shown in the diagram above.
- Connect the LED strip to the LED connector -making sure to match the polarity and attach it to the narrow space of the LED holder.
- Connect positive and negative sides of the LED connector to the positive and negative sides of the DC adapter (respectively). Optionally, add a 50 to 200 Ohm resistor in series with one of the two LED cables to dim the lights.
- Assemble all acrylic parts (except removable parts) using painter's tape and apply acrylic cement or 2-part epoxy. Remove painter's tape after drying.
- Mount camera with lens and attach the usb to a computer running the acquisition software.
- Insert removable walls.
- Place the mouse in the cage.
- Close the lid and power on the LEDs.
See Changelog
© 2021 Leonardo Molina