alma

Automated Limb Motion Analysis (ALMA)

Check out our paper:

Aljovic, A., Zhao, S., Chahin, M. et al. A deep learning-based toolbox for Automated Limb Motion Analysis (ALMA) in murine models of neurological disorders. Commun Biol 5, 131 (2022). https://doi.org/10.1038/s42003-022-03077-6

A behavioral data analysis toolbox for motor research in rodents.

To get started

The program has been tested on Windows, Mac, and Linux systems with Python 3.8, and should function even on low-end laptops. However, at least 8 GB RAM is recommended. Kinematic parameter extraction, particularly dynamic time warping, is computation-intensive and time-consuming, which will vary depending on your data size and hardware.

1. Installation prerequisites: Python 3 (the dependency versions have been verified against Python 3.8 and 3.10, see details below), pip / (mini)conda (Miniconda documentation), (virtual environment / environment manager is recommended)
2. Download / clone this repository to your computer.
3. Open a terminal and navigate to the folder.

   cd Downloads/alma
   

4. Install dependencie in a Python 3.8 environment:

   pip install -r requirements.txt
   

Alternatively, you can install in a Python 3.10 environment. The dependency list is provided for the Conda installer but can easily be adapted to use pip install instead:

conda env create -f conda_env_python_3_10.yml
conda activate venv_python_3_10

1. Ready to go! (Check the command for the correct python version, which could be py, python3, python, …)

   python ./alma.py
   

   Note that if using a Conda environment, you may need to run pythonw instead of python.

Troubleshoot

wxPython might not install at first if the gtk requirements are not met. If you see an error related to wxPython during pip install -r requirements.txt, try

pip install -U -f https://extras.wxpython.org/wxPython4/extras/linux/gtk2/ubuntu-16.04/ wxPython

(https://wxpython.org/blog/2017-08-17-builds-for-linux-with-pip/index.html)

In some cases (particularly some Linux distributions), you might need to install some libraries such as libsdl or libpng12. This problem can be identified by errors when starting the app, such asImportError: libSDL2-2.0.so.0: cannot open shared object file: No such file or directory). Try to solve the ImportError accordingly, e.g.,

sudo apt-get install libsdl2-2.0

and,

sudo add-apt-repository ppa:linuxuprising/libpng12
sudo apt update
sudo apt install libpng12-0

If you run into problem installing, please open an issue with the details (error traces) and your system specs (operating system, python version, …) on Github, and we will get back to you.

Adjusting the GUI display and experiment setups

Open the config.yaml file with a text editor. Here you’ll find the parameters related to the interface display, as well as the default parameters for analyses. If the GUI window isn’t displayed properly at first, you can adjust the window size by editting the window width / height values in config.yaml, saving, and restarting the program.

For more information or support, please visit our wiki page or contact us.

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