siibra-explorer - Interactive 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 an frontend module wrapping around nehuba for visualizing volumetric brain volumes at possible high resolutions, and connecting to siibra-api for offering 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 Interactive Atlas Viewer is available at https://interactive-viewer.apps.hbp.eu. This section is useful for developers who would like to develop this project.

General information

Interactive atlas viewer is built with Angular (v12.0), 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 a http framework.

Develop

Prerequisites

• latest version of node 12.x.x or node 14.x.x

Environments

It is recommended to manage your environments with .env file.

Buildtime environments

Please see build_env.md

Deploy environments

Please see deploy_env.md

e2e test environments

Please see e2e_env.md

Start dev server

To run a dev server, run:

$ git clone https://github.com/HumanBrainProject/interactive-viewer
$ cd interactive-viewer
$ npm i
$ npm run dev-server

Start backend (in a separate terminal):

$ cd deploy
$ node server.js

Build

$ npm run build-aot

Develop plugins

Below demonstrates an example workflow for developing plugins:

$ # build aot version of the atlas viewer
$ npm run build-aot
$ cd deploy
$ # run server with PLUGIN_URLS
$ PLUGIN_URLS=http://localhost:3333/manifest.json;http://localhost:3334/manifest.json node server.js

Interactive Atlas Viewer attempts to fetch list of manifests:

GET {BACKEND_URL}/plugins

The response from this endpoint will be:

[
  "http://localhost:3333/manifest.json",
  "http://localhost:3334/manifest.json"
]

When user launches the viewer, the atlas viewer will attempt to fetch the metadata of the plugins:

GET http://localhost:3333/manifest.json
GET http://localhost:3334/manifest.json

The response from these endpoints are expected to adhere to manifests.

When the user launches the plugin, the viewer will fetch templateUrl and scriptUrl, if necessary.

Plugin developers can start their own webserver, use interactive-viewer-plugin-template, or (coming soon) provide link to a github repository.

plugin readme

plugin api

plugin migration guide

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).