Neuronal Motifs

An interactive tool for querying and visual analysis of network motifs in large connectomics data.

Live Demo

A demo is available here. Before you get started, please add your personal neuprint authentication token under Settings > Auth Token. You can find your token here.

Installation for Local Development

Requirements

• Node.js
• virtualenv

Clone the repository:

git clone https://github.com/jakobtroidl/neuronal-motifs.git && cd neuronal-motifs

Install/activate virtualenv and start the backend:

cd neuronal_motifs/server/
virtualenv -p python3.9 vimo
source vimo/bin/activate
python main.py

From the root directory of the repository, install frontend dependencies and start the frontend:

cd neuronal_motifs/client/
npm install
npm run start

The application is accessible under http://localhost:3000/

Development

• In PyCharm make sure the client and source directory are set as the source root (right click directory > mark directory as > source root)

Download Cache

To render 3D neurons, downloading the neuron data from the data server (https://neuprint.janelia.org/) and computation are required each time. If you want to reduce these loading times, please download the neuron dataset and save it to your local folder.

• Click here to download the cache
• Unzip to neuronal_motifs/server/cache/data/neurons/

Citing

If you find our work helpful, please consider citing it.

@article {troidl2023vimo,
	author = {Troidl, Jakob and Warchol, Simon and Choi, Jinhan and Matelsky, Jordan
    	and Dhanysai, Nagaraju and Wang, Xueying and Wester, Brock and Wei, Donglai
    	and Lichtman, Jeff W and Pfister, Hanspeter and Beyer, Johanna},
	title = {Vimo: Visual Analysis of Neuronal Connectivity Motifs},
	year = {2023},
	doi = {10.1101/2022.12.09.519772},
	publisher = {IEEE},
	URL = {https://www.biorxiv.org/content/10.1101/2022.12.09.519772v2},
	journal = {IEEE Transactions on Visualization and Computer Graphics (IEEE VIS) (to appear)}
}

We gratefully acknowledge the support from NSF award number IIS-2124179.