webKnossos

​ 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​

​​​ ​​ ​​ ​​​

Demo

​https://webknossos.org/​

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 tracing​

• Optimized performance for large tracings

• User and task management for high-throughput crowdsourcing

• Sharing and collaboration features

• ​Standalone datastore component for flexible deployments

• ​Supported dataset formats: WKW, Neuroglancer Precomputed, and BossDB​

• Supported image formats: Grayscale, Segmentation Maps, RGB, Multi-Channel

• ​Support for 3D mesh rendering and on-the-fly isosurface generation​

• ​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, 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.​

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 installations on localhost, please see below.

Development installation

Docker

This is only recommended for local testing. Docker 17+ and Docker Compose 1.18+ are required.

git clone -b master --depth=1 [email protected]:scalableminds/webknossos.git
cd webknossos
docker-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.

Dependencies

• ​Oracle JDK 8+ or Open JDK 8+ (full JDK, JRE is not enough)

• ​sbt​

• ​PostgreSQL 10​

• ​Redis 5+​

• ​node.js 12+​

• ​yarn package manager​

• ​git​

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 [email protected]: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_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 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';"

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.

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

• 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

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

Ask for help in the image.sc community forum.

Contact us at [email protected].

​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

• ​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