siibra-explorer - Interactive atlas viewer for multilevel brain atlases

Authors: Big Data Analytics Group, Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH

Copyright 2020-2021, Forschungszentrum Jülich GmbH

siibra-explorer is a browser based 3D viewer for exploring brain atlases that cover different spatial resolutions and modalities. It is built around an interactive 3D view of the brain displaying a unique selection of detailed templates and parcellation maps for the human, macaque, rat or mouse brain, including BigBrain as a microscopic resolution human brain model at its full resolution of 20 micrometers.

siibra-explorer builds on top nehuba for the visualization volumetric brain volumes at possible high resolutions, and three-surfer for the visualization of surface based atlases. By connecting to siibra-api, siibra-explorer gains access to brain atlases of different species, including to navigate their brain region hierarchies, maps in different coordinate spaces, and linked regional data features. It provides metadata integration with the EBRAINS knowledge graph, different forms of data visualisation, and a structured plugin system for implementing custom extensions.

Getting Started

A live version of the siibra explorer is available at https://atlases.ebrains.eu/viewer/. User documentation can be found at https://siibra-explorer.readthedocs.io/. This README.md is aimed at developers who would like to develop and run siibra-explorer locally.

General information

Siibra explorer is built with Angular (v14.0), Bootstrap (v4), and fontawesome icons. Some other notable packages used are ngrx/store for state management.

Releases newer than v0.2.9 also uses a nodejs backend, which uses passportjs for user authentication, express as the http framework.

Releases newer than v2.13.0 uses a python backend, which uses authlib for user authentication, fastapi as the http framework.

Develop

Prerequisites

• node 16 or later

Environments

Development environments are stored under src/environments/environment.common.ts. At build time, src/environments/environment.prod.ts will be used to overwrite the environment.

Whilst this approach adds some complexity to the development/build process, it enhances developer experience by allowing the static typing of environment variables.

Buildtime environments

Please see build_env.md

Deploy environments

Please see deploy_env.md

e2e test environments

Please see e2e_env.md

Development

To run a frontend dev server, run:

$ git clone https://github.com/FZJ-INM1-BDA/siibra-explorer
$ cd siibra-explorer
$ npm i
$ npm start

To run backend dev server:

$ cd backend
$ pip install -r requirements.txt
$ uvicorn app.app:app --host 0.0.0.0 --port 8080

Test

$ npm run test

Build

$ npm run build

Develop plugins

Please see src/plugin/README.md

Contributing

Feel free to raise an issue in this repo and/or file a PR.

Versioning

Commit history prior to v0.2.0 is available in the legacy-v0.2.0 branch. The repo was rewritten to remove its dependency on neuroglancer and nehuba. This allowed for simpler webpack config, faster build time and AOT compilation.

License

Apache-2.0

Acknowledgements

This software code is funded from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreement No. 945539 (Human Brain Project SGA3).