Walkway data acquisition software

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: - Annotation Software - Paper

Installation

• Install Spinnaker SDK
• Install Python version 3.8 (notice that the only supported Python version is 3.8).
• Open cmd
• Run pip install walkway or python -m pip install walkway.

Usage overview

• 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.capture to start auto-triggering.
• Press q on the GUI or ctrl+c on the command window when done.
• Video files are saved to cmd's working directory (defaults to C:/Users/<your username> in Windows). You may cd to 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 --help for more information.
• Run python -m walkway.gui to open a GUI with a single camera.
• Run python -m walkway.experiment to open an experiment with two FLIR cameras and a Petteron microphone.

Walkway data analysis scripts

MATLAB scripts to analyze data collected with the Walkway setup.

See related resources: - Annotation Software - Paper

Prerequisites

• MATLAB (last tested with R2023a)

Installation

• Install MATLAB
• Download and extract these scripts to Documents/MATLAB folder.

Usage

To export a table with gait metrics: - Create a new data loader to match your DLC data columns (use loadData.m as a reference). - Edit process.m according 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.

Expected configuration

• 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-T20220124110229988302 Sex: 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

Walkway apparatus manufacturing instructions

CAD files and assembly instructions for a Walkway apparatus.

See related resources: - Annotation Software - Paper

Components

• 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)

Assembly instructions

• 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.

Usage

• Insert removable walls.
• Place the mouse in the cage.
• Close the lid and power on the LEDs.

Changelog

See Changelog

License

© 2021 Leonardo Molina

License for the aparatus and CAD files

Creative Commons BY-NC-SA 4.0 License.

License for the source code

GNU GPLv3 License.