Module for analysis of 3D animal pose sequences. Based on work by Berman et al. (2014) and Marshall et al. (2020).
Install the latest version of Miniconda on your machine.
The following steps will clone this repository, set up your conda environment, and install neuroposelib.
Use environment.yml if you're on a Linux machine, and environment_osx.yml for Mac.
git clone https://github.com/joshuahwu/neuroposelib.git
cd neuroposelib
conda env create -n neuroposelib -f environment.yml
conda activate neuroposelib
conda install -c conda-forge opentsne
pip install -e .
Note that pip and setuptools must be updated to the most recent versions.
To begin gaining familiarity with the functionality of this package, download the demo dataset at this link or with the command line as follows:
cd neuroposelib
wget -v -O ./tutorials/demo_mouse.zip -L https://duke.box.com/shared/static/2ypagjda3gws3m0yqzzdrszb79yfznz8.zip
unzip ./tutorials/demo_mouse.zip -d ./tutorials/
rm ./tutorials/demo_mouse.zip
and run through the code in /tutorials/tutorial.ipynb.
- Joshua Wu - [email protected]