Install ffmpeg
First, check to see if you have ffmpeg installed by typing the following in the terminal:
ffmpeg -version
If not, install:
sudo apt install ffmpeg
Set up a conda environment
NOTE: do not do this if you are setting up this repo in a Lightning Studio.
conda create --yes --name labeler python=3.10
conda activate labeler
Install dependencies
Lightning Pose:
git clone https://github.com/danbider/lightning-pose.git
cd lightning-pose
pip install -e .
cd ..
Ensemble Kalman Smoother:
git clone https://github.com/paninski-lab/eks.git
cd eks
pip install -e .
cd ..
Install lp3d-analysis package locally
git clone https://github.com/paninski-lab/lp3d-analysis.git
cd lp3d-analysis
pip install -e .
cd ..
python pipelines/run_pipeline.py --config <path_to_pipeline_config>