SNUB is a visual interface for systems neuroscience. Using a set of linked data-views, users can explore relationships between raw video, 3D animal pose, behavior annotations, neural activity, or any other relevant time-series data.
Create and activate a new conda environment with python≥3.8, clone this repo, and install via pip
conda create -n snub python=3.8
conda activate snub
git clone https://github.com/calebweinreb/SNUB.git
pip install -e SNUB
To speed up selections, pip install ncls. To use the 3D mesh viewer, install pip install PyOpenGL PyOpenGL_accelerate. The docs include more detailed installation instructions.
- Download the example project.
- Launch SNUB from the command line with the command
snub. - Go to
File > Open Project, navigate to the project directory, and hitChoosewith the directory selected. - Alternatively, launch SNUB directly with the project path
snub /path/to/project/directory.
Loading data is simple with the snub.io module. For example the following code creates a new project with paired electrophysiology and video data. See the Tutorial for more details.
import snub.io
project_directory = 'path/to/new/project'
snub.io.project.create_project(project_directory, duration=1800)
snub.io.project.add_video(project_directory, 'path/to/my_video.avi', name='IR_camera')
snub.io.project.add_splikeplot(project_directory, 'my_ephys_data', spike_times, spike_labels)