Code Readme

Last updated 6 months ago


Cellular-resolution connectomics is currently substantially limited by the throughput and efficiency of data analysis. Current solutions require an efficient integration of automated image analysis with massive manual data annotation. To scale such annotation efforts it is decisive to be able to crowd source data analysis online. Here we present webKnossos.

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.

webKnossos logo




Development setup


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.


See the wiki for instructions on updating this try setup.



If you are using OS X try using this awesome installer:

Or install Java manually and run:

# Install Homebrew package manager
/usr/bin/ruby -e "$(curl -fsSL"
# Install git, node.js, postgres, sbt, gfind, gsed
brew install git node postgresql sbt findutils coreutils gnu-sed
npm install -g yarn
# Start postgres
brew services start postgresql
# Create PostgreSQL user
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

Ubuntu 16.04 LTS

# Adding repositories for sbt, nodejs and yarn
echo "deb /" | sudo tee /etc/apt/sources.list.d/sbt.list
sudo apt-key adv --keyserver hkp:// --recv 642AC823
echo "deb xenial-pgdg main" | sudo tee /etc/apt/sources.list.d/postgresql.list
curl -sS | sudo apt-key add -
curl -sL | sudo -E bash -
curl -sS | sudo apt-key add -
echo "deb 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
# 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


  • Install Java JDK 8 (from Oracle or OpenJDK)

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




node.js & yarn

Run locally

yarn start

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

Production setup

See wiki for recommended production setup.

For upgrades, please check the changelog & migration guide.


# 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

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


webKnossos was inspired by KNOSSOS.


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

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