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 - On your own server - User Documentation - Contact us
Exploration of large 3D image datasets
Fully browser-based user experience with efficient data streaming
Creation/editing of skeleton and volume annotations
Optimized performance for large tracings
User and task management for high-throughput crowdsourcing
Sharing and collaboration features
Standalone datastore component for flexible deployments
Supported image formats: Grayscale, Segmentation Maps, RGB, Multi-Channel
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
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.
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 installations on localhost, please see below.
This is only recommended for local testing. Docker 17+ and Docker Compose 1.18+ are required.
git clone -b master --depth=1 git@github.com:scalableminds/webknossos.gitcd webknossosdocker-compose pull webknossos./start-docker.sh
Open your local webknossos instance on localhost:9000 and complete the onboarding steps in the browser. Now, you are ready to use your local webKnossos instance.
See the wiki for instructions on updating this development setup.
For non-localhost deployments, check out the installation guide in the documentation.
Oracle JDK 8+ or Open JDK 8+ (full JDK, JRE is not enough)
sbt
Redis 5+
git
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, gsedbrew install git node postgresql sbt findutils coreutils gnu-sed redisnpm install -g yarn# Start postgresbrew services start postgresql# Create PostgreSQL usercreatedbpsql -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 repositorygit clone git@github.com:scalableminds/webknossos.git
# Adding repositories for sbt, nodejs and yarnecho "deb https://dl.bintray.com/sbt/debian /" | sudo tee /etc/apt/sources.list.d/sbt.listsudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv 642AC823echo "deb http://apt.postgresql.org/pub/repos/apt/ xenial-pgdg main" | sudo tee /etc/apt/sources.list.d/postgresql.listcurl -sS https://www.postgresql.org/media/keys/ACCC4CF8.asc | sudo apt-key add -curl -sL https://deb.nodesource.com/setup_12.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 everythingsudo apt-get updatesudo apt-get install -y git postgresql-10 postgresql-client-10 nodejs scala sbt openjdk-8-jdk yarn redis-server# Assign a password to PostgreSQL usersudo -u postgres psql -c "ALTER USER postgres WITH ENCRYPTED PASSWORD 'postgres';"
If you already have a different Java version installed, set the default version to Java 8:
run sudo update-alternatives --config java
when prompted, select the desired version
On older Ubuntu distributions: Please make sure to have the correct versions of node, PostgreSQL and java installed.
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
Install PostgreSQL from https://www.postgresql.org/download/
PostgreSQL version 10+ is required
Redis
Install Redis from https://redis.io/download
node.js & yarn
Install node from http://nodejs.org/download/
node version 12+ is required
Install yarn package manager: npm install -g yarn
yarn installyarn 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.
For upgrades, please check the changelog & migration guide.
# Frontend lintingyarn run lint# Format frontend codeyarn run pretty# Frontend type checkingyarn flow# Frontend testsyarn test-verbose# End-to-end testsdocker-compose run e2e-tests
Contact us at hello@scalableminds.com.
scalable minds offers commercial hosting, support and development services for webKnossos.
scalable minds - https://scalableminds.com/
Max Planck Institute for Brain Research – https://brain.mpg.de/
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
AGPLv3