Code Readme

webKnossos

webKnossos Logo webKnossos is an open-source tool for annotating and exploring large 3D image datasets.

  • Fly through your data for fast skeletonization and proof-reading

  • 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 - User Documentation - Contact us

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Demo

https://webknossos.org/

Features

Publication

Boergens, Berning, Bocklisch, Bräunlein, 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.

Development installation

Docker

This is the fastest way to try webKnossos. Docker CE 17+ and Docker Compose 1.18+ is required. This is only recommended for testing. For production, a more elaborate setup with persistent file mounts and HTTPS reverse proxy is recommended.

git clone -b master --depth=1 git@github.com:scalableminds/webknossos.git
cd webknossos
docker-compose pull webknossos
./start-docker.sh

Open your local webknossos instance on localhost:9000.

See the wiki for instructions on updating this try setup.

Dependencies

OS X

If you are using OS X try using this awesome installer: https://gist.github.com/normanrz/9128496

Or install Java manually and run:

# Install Homebrew package manager
/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
# Install git, node.js, postgres, sbt, gfind, gsed
brew install git node postgresql sbt findutils coreutils gnu-sed redis
npm install -g yarn
# Start postgres
brew services start postgresql
# Create PostgreSQL user
createdb
psql -c "CREATE DATABASE webknossos;"
psql -c "CREATE USER postgres WITH ENCRYPTED PASSWORD 'postgres';"
psql -c "ALTER USER postgres WITH SUPERUSER;"
psql -c "GRANT ALL PRIVILEGES ON DATABASE webknossos TO postgres;"
# Checkout the webKnossos git repository
git clone git@github.com:scalableminds/webknossos.git

Ubuntu 16.04 LTS

# Adding repositories for sbt, nodejs and yarn
echo "deb https://dl.bintray.com/sbt/debian /" | sudo tee /etc/apt/sources.list.d/sbt.list
sudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv 642AC823
echo "deb http://apt.postgresql.org/pub/repos/apt/ xenial-pgdg main" | sudo tee /etc/apt/sources.list.d/postgresql.list
curl -sS https://www.postgresql.org/media/keys/ACCC4CF8.asc | sudo apt-key add -
curl -sL https://deb.nodesource.com/setup_10.x | sudo -E bash -
curl -sS https://dl.yarnpkg.com/debian/pubkey.gpg | sudo apt-key add -
echo "deb https://dl.yarnpkg.com/debian/ stable main" | sudo tee /etc/apt/sources.list.d/yarn.list
# Installing everything
sudo apt-get update
sudo apt-get install -y git postgresql-10 postgresql-client-10 nodejs scala sbt openjdk-8-jdk yarn redis-server
# Assign a password to PostgreSQL user
sudo -u postgres psql -c "ALTER USER postgres WITH ENCRYPTED PASSWORD 'postgres';"

On older Ubuntu distributions: Please make sure to have the correct versions of node, PostgreSQL and java installed.

Manual Installation

Java

  • Install Java JDK 8 (from Oracle or OpenJDK)

  • make sure JAVA_HOME and JDK_HOME are set and PATH contains path to JDK

sbt

See: http://www.scala-sbt.org/release/docs/Getting-Started/Setup.html

PostgreSQL

Redis

node.js & yarn

Run locally

yarn install
yarn start

Will fetch all Scala, Java and node dependencies and run the application on Port 9000. Make sure that the PostgreSQL and Redis services are running before you start the application.

Upgrades

For upgrades, please check the changelog & migration guide.

Tests

# Frontend linting
yarn run lint
# Format frontend code
yarn run pretty
# Frontend type checking
yarn flow
# Frontend tests
yarn test-verbose
# End-to-end tests
docker-compose run e2e-tests

Contact and support

Contact us at hello@scalableminds.com.

scalable minds offers commercial hosting, support and development services for webKnossos.

Credits

webKnossos was inspired by KNOSSOS.

Thanks

  • CircleCI for letting us run builds and tests on their CI

  • Browser Stack for letting us test WebKnossos on a variety of different devices

License

AGPLv3