Appendix A — Prerequisites

A.1 Knowledge

We assume basic familiarity with Python, ideally including its core scientific libraries such as NumPy, Pandas, Matplotlib, and Jupyter.

A.2 Hardware

This is a hands-on course, so please bring your own laptop and charger.
A mouse is strongly recommended, especially for tasks like image annotation.
A dedicated GPU is not required, though it may speed up some computations.

A.3 Software

You’ll need both general tools for Python programming and specific software required for the course, as detailed below.

A.3.1 General development tools

Note

If you already have a working Anaconda or Miniconda installation and have used it to run Python scripts or Jupyter notebooks, you can likely skip the steps below.

To prepare your computer for Python development, we recommend following the Software Carpentries installation instructions, in particular:

You’ll also need a code editor (IDE) configured for Python.
If you already have one you’re comfortable with, feel free to use it. Otherwise, we recommend:

A.3.2 For the SLEAP tutorial

Please install SLEAP following the official installation instructions.

Note

For this workshop, use SLEAP version 1.3.4. Be sure to replace the default version number (e.g. 1.4.1) in the instructions with 1.3.4.

This should create a conda environment named sleap with the necessary dependencies. You can verify the installation by running:

conda activate sleap
sleap-label

This should launch the SLEAP graphical user interface (GUI).

A.3.3 For the interactive notebooks

You will also need a separate conda environment with everything required for the interactive exercises, including the movement and jupyter packages.

We recommend cloning this workshop’s repository and creating the environment using the provided environment.yaml file:

git clone https://github.com/neuroinformatics-unit/animals-in-motion.git
cd animals-in-motion
conda env create -n animals-in-motion-env -f environment.yaml

To test your setup, run:

conda activate animals-in-motion-env
movement launch

This should open the movement GUI, i.e. the napari image viewer with the movement plugin docked on the right.

Note

There are other ways to install the movement package.
However, for this workshop, we recommend using the environment.yaml file to ensure that all necessary dependencies, including those beyond movement, are included.

A.4 Data

Bringing your own data is encouraged but not required. This could include video recordings of animal behaviour and/or motion tracking data you’ve previously generated.

We also provide some example datasets for you to use during the workshop. Please download these from Dropbox before the workshop starts (they are a few GB in size).