Quantifying Animal Behaviour

Download example data, clips and external packages:

Download: Shared OneDrive Folder

Inside you will find a Data folder and an ExternalPackages folder containing the cudnn and tensorflow packages. Copy both folders to the root of the repository. You will need them later...

Install instructions

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Install third party SLEAP dependencies (Optional)

NOTE: This step is optional for hardware acceleration IF you have a compatible NVidia card. If not, or for slow workflow but easier install, skip this bit.

(Full instructions, but we shouldn't need this!)

In order to use the graphics card for hardware accelerated inference in Bonsai, you will need to install the Cuda Toolkit 11.3 (for SLEAP multi-animal tracking)

• Select Custom install and check CUDA > Development and CUDA > Runtime ONLY (uncheck everything else)

Once installed, could be worth checking your User and System Variables. You should see your Python 3.10 installation on the path of User Variables. You should see the CUDA_PATH is correctly pointing to CUDA 11.3, and the Cuda/bin folder is on the system variables path.

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Bonsai

• In a command terminal, run setup.cmd from the .bonsai folder . This will run the powershell script setup.ps1 to automatically intall a local Bonsai installation you can use to edit and run the Workflows in this project

Set up python environment for Bonsai.ML

1. (Recommended) Visual Studio Code

Direct Download: python 3.10 (Windows 64-bit installer) Python release page

Hit Ctrl-P to bring up the command pallette. Choose Python: Create Environment..., then Venv. Choose your Python 3.10 installation as the interpreter path, and check the requirements.txt.

Done. If you now open a new Powershell terminal, the environment will activate automatically.

2. (Optional) From a command line terminal:

Install virtual env if needed

pip install virtualenv

Create the virtual environment

python -m venv .venv
.venv\Scripts\activate
pip install -r requirements.txt

Run Bonsai from the command line terminal:

.\.bonsai\Bonsai.exe

Open the workflows!

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Clone BonFly (uses Bonsai 2.9.1 preview)

git clone https://github.com/jfrazao/BonFly.git

Install Bonsai by running the setup.cmd in the .\bonsai folder

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Package Development Working Environment

Visual Studio Community (optional)

1. Download and run Visual Studio Community.
2. Check .NET Desktop Development workload
3. (optional) uncheck IntelliCode support.

Bonsai VS Extensions.

From the Windows Start Menu, search for the "Install Bonsai VS Extensions" shortcut and run it.

Child process debugging

1. Download and install Microsoft Child Process Debugging Power Tool.
2. For each project:
   • Ensure that launchSettings.json is set to "nativeDebugging": true.
   • Enable child process debugging in the Debug > Other Debug Targets > Child Process Debugging Settings.

Launch Visual Studio, and set some options up:

Navigate to TOOLS->Options->Debugging->General and disable "Require source files to exactly match the original version" .

Go to TOOLS->Options->Debugging->Symbols and enable the Microsoft Symbols Server. Finally, under TOOLS->Options->Debugging, check "Enable Just My Code' and "use Manage/Unmanage mode".

Visual Studio Code

1. Download and run Visual Studio Code.
2. Make sure "Add to PATH" option is checked.

Git for Windows

1. Download and run Git for Windows.
2. Select components: uncheck all except Git LFS.
3. Default editor: Visual Studio Code.
4. Override default branch name: main
5. Choose "Git from the command line and also from 3rd party software".
6. Use bundled OpenSSH.
7. Use native Windows Secure Channel library.
8. Checkout Windows-style, commit Unix-style line endings.
9. Use default console window.
10. Default (fast-forward or merge).
11. Use default Git credential manager.
12. Leave at defaults for everything else.
13. Open command prompt (cmd.exe) or PowerShell.
14. Configure git user and email