siibra-explorer

https://github.com/fzj-inm1-bda/siibra-explorer

Science Score: 54.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
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Academic publication links
Links to: zenodo.org
✓
Committers with academic emails
3 of 7 committers (42.9%) from academic institutions
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Institutional organization owner
Organization fzj-inm1-bda has institutional domain (www.fz-juelich.de)
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (13.4%) to scientific vocabulary

Last synced: 7 months ago · JSON representation

Repository

Basic Info

Host: GitHub
Owner: FZJ-INM1-BDA
License: apache-2.0
Language: TypeScript
Default Branch: master
Size: 67.8 MB

Statistics

Stars: 25
Watchers: 7
Forks: 5
Open Issues: 62
Releases: 108

Created over 8 years ago · Last pushed 8 months ago

Metadata Files

Readme License Codemeta

siibra-explorer - Interactive atlas viewer for multilevel brain atlases

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

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

To run backend dev server:

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

Test

bash $ npm run test

Build

bash $ 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).

Owner

Name: Big Data Analytics group
Login: FZJ-INM1-BDA
Kind: organization
Location: Jülich, Germany

Website: https://www.fz-juelich.de/inm/inm-1/EN/Forschung/Big_Data_Analytics/Big_Data_Analytics_node.html
Repositories: 35
Profile: https://github.com/FZJ-INM1-BDA

Big Data Analytics group at the Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Juelich

CodeMeta (codemeta.json)

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  "dateCreated": "2024-08-28",
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  "datePublished": "2019-04-26",
  "description": "`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. ",
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GitHub Events

Total

Create event: 6
Issues event: 14
Release event: 9
Watch event: 2
Issue comment event: 83
Push event: 133
Pull request review event: 2
Pull request review comment event: 3
Pull request event: 18
Fork event: 1

Last Year

Create event: 6
Issues event: 14
Release event: 9
Watch event: 2
Issue comment event: 83
Push event: 133
Pull request review event: 2
Pull request review comment event: 3
Pull request event: 18
Fork event: 1

Committers

Last synced: 11 months ago

All Time

Total Commits: 2,608
Total Committers: 7
Avg Commits per committer: 372.571
Development Distribution Score (DDS): 0.144

Past Year

Commits: 121
Committers: 2
Avg Commits per committer: 60.5
Development Distribution Score (DDS): 0.008

Top Committers

Name	Email	Commits
Xiao Gui	x**3@g**m	2,232
fsdavid	d**1@m**m	327
Christian Schiffer	c**r@f**e	24
Timo Dickscheid	t**d@f**e	17
fsdavid	g**a@l**u	5
Ahmet Nihat Simsek	a**k@g**m	2
Piotr Majka	p**a@n**l	1

Committer Domains (Top 20 + Academic)

fz-juelich.de: 2 nencki.edu.pl: 1 live.ru: 1 mail.com: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time

Total issues: 47
Total pull requests: 60
Average time to close issues: about 2 years
Average time to close pull requests: about 1 month
Total issue authors: 9
Total pull request authors: 5
Average comments per issue: 1.98
Average comments per pull request: 2.9
Merged pull requests: 54
Bot issues: 0
Bot pull requests: 4

Past Year

Issues: 13
Pull requests: 17
Average time to close issues: about 17 hours
Average time to close pull requests: 4 days
Issue authors: 5
Pull request authors: 2
Average comments per issue: 0.69
Average comments per pull request: 3.24
Merged pull requests: 17
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

xgui3783 (23)
PolarBean (9)
fsdavid (3)
Majpuc (3)
SBludau (3)
KimLothmann (3)
AhmetNSimsek (2)
dickscheid (2)
pmajka (1)

Pull Request Authors

xgui3783 (69)
fsdavid (4)
dependabot[bot] (4)
baishi (2)
AhmetNSimsek (1)

Top Labels

Issue Labels

feature request (14) bug (7) blocked (1) regression (1) important (1) M20 (1) quality of life (1) needs test (1) question (1)

Pull Request Labels

dependencies (4)

Dependencies

.github/workflows/ci.yml actions

actions/checkout v2 composite
actions/setup-node v1 composite

.github/workflows/docker_img.yml actions

actions/checkout v2 composite

.github/workflows/e2e.yml actions

actions/checkout v2 composite
actions/upload-artifact v2 composite

.github/workflows/manual_e2e.yml actions

actions/checkout v2 composite
actions/github-script v5 composite

.github/workflows/release-ci.yml actions

actions/checkout v1 composite

.github/workflows/release.yml actions

actions/checkout v1 composite
actions/create-release v1 composite
actions/upload-release-asset v1 composite

.github/workflows/repo_sync_ebrains.yml actions

actions/checkout v2 composite
wei/git-sync v3 composite

Dockerfile docker

node 16 build
node 16-alpine build
ubuntu 22.04 build

docs/Dockerfile docker

nginx alpine build
python 3.7 build

package-lock.json npm

1803 dependencies

package.json npm

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@angular/cli ^14.2.10 development
@angular/compiler-cli ^14.2.12 development
@babel/core ^7.17.5 development
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@storybook/testing-library 0.0.13 development
@types/jasmine ~3.8.0 development
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typescript ^4.8.4 development
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@angular/core ^14.2.12
@angular/forms ^14.2.12
@angular/material ^14.2.7
@angular/platform-browser ^14.2.12
@angular/platform-browser-dynamic ^14.2.12
@angular/router ^14.2.12
@ngrx/effects ^14.3.2
@ngrx/store ^14.3.2
acorn ^8.4.1
export-nehuba 0.0.12
file-loader ^6.2.0
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rxjs ~6.6.0
showdown ^2.0.0
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docs-requirements.txt pypi

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mkdocs >=1.1,<2
mkdocs-material *

.github/workflows/deploy-on-okd.yml actions

.github/workflows/on_branch_del.yml actions

src/res/icons/meta.json cpan

docs/develop/docker-compose.yml docker

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docker-registry.ebrains.eu/siibra/siibra-explorer dev-local-10081
redis latest

backend/requirements.txt pypi

authlib *
fastapi *
httpx *
itsdangerous *
markdown *
redis *
uvicorn *