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Installations and set up

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Hannah L edited this page Oct 10, 2023 · 10 revisions

We recommend installing deeplabcut and SimBA in different anaconda environments as these software programs have different dependency requirements. This workflow has been tested on Windows 11.

Deeplabcut

Our models were generated with deeplabcut version 2.3.0, but should be compatible with newer versions. Please follow the instructions for installing deeplabcut provided on their installation documentation page. We recommend testing new installations using the deeplabcut test script.

SimBA

Behavioral classifiers were generated using SimBA version 1.31.2, have been successfully tested in SimBA 1.55.6, and should work with newer versions as well. Please follow the SimBA installation guide.
Note: with SimBA version 1.55.6, please also run pip install numba==0.52.0 after SimBA installation

Install the circle-fit package

The AMBER custom feature extraction script uses a functions from the circle-fit package. This package is not automatically added during SimBA installation, so it needs to be installed separately in the SimBA environment.
To do this, activate the SimBA anaconda environment
e.g. conda activate simbaenv
Then install the circle-fit package:
pip install circle-fit

Download AMBER scripts

  1. The pose estimation models and scripts required for the AMBER pipeline can be found in this github repository and on our OSF repository. You should download all scripts as a zip file or by cloning the repository.
    git clone https://github.com/lapphe/AMBER-pipeline.git

git download small

  1. You will need to update the AMBER SimBA project config file to reflect the specific location of the project files on your computer. To do this, find the project_config.ini file located in AMBER-pipeline/SimBA_AMBER_project/project_folder/. Double click to open the file in a text editor. The project_path (line 2) and model_dir (line 8) need to be updated to reflect the current location.

For example, if the AMBER-pipeline folder is located on your Desktop, changing the path might look similar to the image below:

simba config small

  1. The behavioral classifiers are large files and cannot be stored on github. Please download them from our OSF repository.
    OSF download small

  2. Unzip/extract the behavior model files (e.g. using 7 zip)

  3. Move the behavior classification models to the “models” folder in AMBER-pipeline/SimBA_AMBER_project/models. This is inside the directory cloned from the AMBER github repository

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