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Xiao Gui authored
maint: updated repo README.md maint: typo, update k8s configmap value, cleaned up env var maint: plugin API documentation fix: plugin API generation maint: use stable as default siibra-api endpoint maint: add git repo to mkdocs
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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).