webknossos
Visualize, share and annotate your large 3D images online
Science Score: 49.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 1 DOI reference(s) in README -
✓Academic publication links
Links to: nature.com -
○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (13.9%) to scientific vocabulary
Keywords
connectomics
em
hacktoberfest
microscopy
microscopy-images
neurobiology
reconstruction
Last synced: 6 months ago
·
JSON representation
Repository
Visualize, share and annotate your large 3D images online
Basic Info
- Host: GitHub
- Owner: scalableminds
- License: agpl-3.0
- Language: TypeScript
- Default Branch: master
- Homepage: https://webknossos.org
- Size: 762 MB
Statistics
- Stars: 155
- Watchers: 14
- Forks: 29
- Open Issues: 477
- Releases: 113
Topics
connectomics
em
hacktoberfest
microscopy
microscopy-images
neurobiology
reconstruction
Created almost 14 years ago
· Last pushed 6 months ago
Metadata Files
Readme
Changelog
Contributing
License
Citation
README.md
WEBKNOSSOS
WEBKNOSSOS is an open-source tool for annotating and exploring large 3D image datasets.
- Fly through your data for fast skeletonization and proofreading
- Create 3D training data for automated segmentations efficiently
- Scale data reconstruction projects with crowdsourcing workflows
- Share datasets and annotations with collaborating scientists
Start using WEBKNOSSOS - On your own server - User Documentation - Contact us
Website and hosted version
Features
- Exploration of large 3D image datasets
- Fully browser-based user experience with efficient data streaming
- Creation/editing of skeleton and volume annotations
- Innovative flight mode for fast skeleton annotation
- Optimized performance for large annotations
- User and task management for high-throughput crowdsourcing
- Sharing and collaboration features
- Proofreading tools for working with large (over)-segmentations
- Standalone datastore component for flexible deployments
- Supported dataset formats: WKW, Neuroglancer Precomputed, Zarr, N5
- Supported image formats: Grayscale, Segmentation Maps, RGB, Multi-Channel
- Support for 3D mesh rendering and ad-hoc mesh generation
- Export and streaming of any dataset and annotation as Zarr to third-party tools
- Documented frontend API for user scripts, REST API for backend access
- Open-source development with automated test suite
- Docker-based deployment for production and development
- Detailed Documentation
Publication
Boergens, Berning, Bocklisch, Brunlein, Drawitsch, Frohnhofen, Herold, Otto, Rzepka, Werkmeister, Werner, Wiese, Wissler and Helmstaedter webKnossos: efficient online 3D data annotation for connectomics. Nature Methods (2017) DOI:10.1038/NMETH.4331.
Read more about the original publication.
Installation
WEBKNOSSOS is open-source, so you can install it on your own server.
Check out the documentation for a tutorial on how to install WEBKNOSSOS on your own server.
For development installations, please see DEV_INSTALL.md file.
Contributions, Contact and Support
We welcome community feedback and contributions! We are happy to have
- general feedback, observations and questions on the image.sc forum,
- feature suggestions and bug reports as issues on GitHub,
- documentation, examples and code contributions as pull requests on GitHub.
For details on community contributions, please refer to our Contributing guide.
Contact us at hello@webknossos.org.
scalable minds offers commercial hosting, support and development services for WEBKNOSSOS.
Credits
- scalable minds - https://scalableminds.com/
- Max Planck Institute for Brain Research https://brain.mpg.de/
WEBKNOSSOS was inspired by KNOSSOS.
Thanks
- Browser Stack for letting us test WEBKNOSSOS on a variety of different devices
- CircleCI for letting us run builds and tests on their CI
License
AGPLv3
Owner
- Name: scalable minds
- Login: scalableminds
- Kind: organization
- Email: hello@scalableminds.com
- Location: Germany
- Website: https://scalableminds.com
- Twitter: scalableminds
- Repositories: 109
- Profile: https://github.com/scalableminds
Dependencies
docker-compose.yml
docker
- postgres 10-alpine
- redis 5.0
- scalableminds/fossildb master__410
- scalableminds/puppeteer master
- scalableminds/webknossos ${DOCKER_TAG
- scalableminds/webknossos-connect master__205
- scalableminds/webknossos-datastore ${DOCKER_TAG
- scalableminds/webknossos-dev latest
- scalableminds/webknossos-tracingstore ${DOCKER_TAG
.github/workflows/build_test_deploy.yml
actions
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.github/workflows/codespell.yml
actions
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- codespell-project/actions-codespell v2 composite
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.github/workflows/nightly.yml
actions
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.github/workflows/wkorg-nightly.yaml
actions
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- actions/upload-artifact v3 composite
.github/actions/retry/action.yml
actions
.github/docker-compose.yml
docker
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- redis 7.4
- scalableminds/fossildb master__510
- scalableminds/webknossos ${DOCKER_TAG}
- scalableminds/webknossos-datastore ${DOCKER_TAG}
- scalableminds/webknossos-tracingstore ${DOCKER_TAG}
tools/hosting/docker-compose.yml
docker
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webknossos-datastore/deployment/docker-compose.yml
docker
- redis 5.0-alpine
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webknossos-tracingstore/deployment/docker-compose.yml
docker
- redis 5.0-alpine
- scalableminds/fossildb ${FOSSILDB_TAG}
- scalableminds/fossildb-client ${FOSSILDB_TAG}
- scalableminds/webknossos-tracingstore ${DATASTORE_TAG}
package.json
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