Table of Contents

Software Installation

The task's software is composed by the Bonsai workflow, which contains the task logic, and by small Python scripts that perform some operations at the beginning and at the end of the a session (namely, parsing both input and output files from/to more human readable formats). In order to facilitate the deployment of the project and with reproducibility in mind, the Bonsai workflow was developed inside a Bonsai environment and the Python scripts uses uv to create and maintain the Python virtual environment.

To install the task's software, follow the steps:

  1. Download the source code from the latest project release and unzip it. Alternatively, clone the repository.
  2. Run ./Setup.cmd to install the Bonsai environment, the Python environment and FFmpeg and to download the necessary configuration files (template.yml, setup.csv, training.csv) into ./config directory (in case these don't exist already). An application window will appear which is used to specify the setup number, the COM port of each Harp device and the paths to the configuration files and output directory. Configuration GUI
    1. Select the setup number.
    2. Specify the serial port that corresponds to each Harp device.
      • The setup doesn't require a Harp CurrentDriver to work. This device is only used in optogenetics sessions, so if this is not going to be the use case, the serial port for this device can be ignored.
    3. Select the paths to the different input and output files.
      • The configuration files downloaded to the ./config directory can be moved elsewhere.
      • The template.yml must be inside the animal config directory!
      • The animal config directory is where the [animal_id].yml file of each animal will be created inside the corresponding batch folder.
      • The output backup directory is optional. Video-related data will not be saved to this directory.
    4. Click on the Update Configuration button, which will create the ./src/config/config.yml file, which is required to run the task.
      • Please don't move or delete the ./src/config/config.yml file! If, for some reason, any of the paths or COM ports need to be changed, re-run the Setup.cmd script.
    5. To upload the sounds to the Harp SoundCard, start by selecting the files containing calibration parameters and EQ filter of each speaker. These files should have the .npy extension and were generated during speaker calibration procedure.
    6. Optional: Select the number of sounds to be uploaded to the Harp SoundCard.
    7. Click on the Upload Sounds button and wait until the process is finished (the button will be enabled again when it happens). The uploaded sounds are 10-second white noises with a sampling rate of 192 kHz.

Camera Drivers

In order to run the Bonsai workflow that contains the task's logic, the camera drivers for the setup's camera must be installed. Instructions to install the drivers for both FLIR and Point Grey cameras can be found below.

FLIR

In order to use the FLIR camera to record the sessions, install the Spinnaker drivers. It's mandatory that the computer has the version 1.29.0.5 of the drivers installed, since the version supported by Spinnaker Bonsai Package. After opening the installer, follow the steps below:

  1. Click on Next. Then, accept the terms and click on Next again.
  2. Select Application Development and click on Next.
  3. Deselect GigE Driver and click on Next.
  4. Deselect the I will use GigE Cameras. checkbox and click on Next.
  5. Finally, click on Install.

Point Grey

In order to use the Point Grey camera to record the sessions, install the FlyCap2 drivers (version 2.11.3.425). After opening the installer, follow the steps below:

  1. Select FlyCapture2_x64.msi and click on Install.
  2. Click on Next. Then, accept the terms and click on Next again, twice.
  3. Deselect the Automatically register with PGR via the internet checkbox and click on Next, twice, again.
  4. Click on Complete.
  5. Select the I will use USB cameras checkbox and click on Next.
  6. Select the Click to confirm checkbox and click on Next, twice.
  7. Finally, click on Install.

FFmpeg

The task's code makes use of the FFmpeg software to save the video recordings in the disk, because it allows the video to be recorded with higher framerates, without loss of image quality and by making a better use of the computer's resources than the native VideoWriter Bonsai node.

FFmpeg can be installed with WinGet by running the following command in the Terminal:

winget install Gyan.FFmpeg
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