GitBook: [docs] 23 pages and 27 assets modified

README.md

@@ -1,20 +1,21 @@
-# webKnossos
-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**.
+# Introduction
+
+## webKnossos
+
+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.](https://www.nature.com/articles/nmeth.4331)
+> webKnossos: efficient online 3D data annotation for connectomics.  
+> [Nature Methods \(2017\) DOI:10.1038/NMETH.4331.](https://www.nature.com/articles/nmeth.4331)
+
+![webKnossos logo](https://webknossos.brain.mpg.de/assets/images/oxalis.svg) [![CircleCI](https://circleci.com/gh/scalableminds/webknossos.svg?style=svg)](https://circleci.com/gh/scalableminds/webknossos)
 
-![webKnossos logo](https://webknossos.brain.mpg.de/assets/images/oxalis.svg)
-[![CircleCI](https://circleci.com/gh/scalableminds/webknossos.svg?style=svg)](https://circleci.com/gh/scalableminds/webknossos)
+### Demo
 
-## Demo
 [https://demo.webknossos.org/](https://demo.webknossos.org/)
 
-## Features
+### Features
+
 * Exploration of large 3D image datasets
 * Fully browser-based user experience with efficient data streaming
 * Creation/editing of skeleton and volume annotations
@@ -23,37 +24,35 @@ webKnossos: efficient online 3D data annotation for connectomics.
 * User and task management for high-throughput crowdsourcing
 * Sharing and collaboration features
 * [Standalone datastore component](https://github.com/scalableminds/webknossos/tree/master/webknossos-datastore) for flexible deployments
-* [Supported dataset formats: WKW (Optimized), KNOSSOS cubes](https://github.com/scalableminds/webknossos/wiki/Datasets)
+* [Supported dataset formats: WKW \(Optimized\), KNOSSOS cubes](https://github.com/scalableminds/webknossos/wiki/Datasets)
 * Supported image formats: Grayscale, Segmentation Maps, RGB, Multi-Channel
 * [Documented frontend API for user scripts](https://demo.webknossos.org/assets/docs/frontend-api/index.html), REST API for backend access
 * Open-source development with [automated test suite](https://circleci.com/gh/scalableminds/webknossos)
 * [Docker-based deployment](https://hub.docker.com/r/scalableminds/webknossos/) for production and development
 
+### Development setup
+
+#### Docker
 
-## Development setup
-### 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](https://github.com/scalableminds/webknossos/wiki/Production-setup), a more elaborate setup with persistent file mounts and HTTPS reverse proxy is recommended.
+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](https://github.com/scalableminds/webknossos/wiki/Production-setup), a more elaborate setup with persistent file mounts and HTTPS reverse proxy is recommended.
 
 ```bash
 docker-compose pull webknossos
 docker-compose up webknossos
 ```
 
-### Dependencies
+#### Dependencies
 
-* [Oracle JDK 8+](http://www.oracle.com/technetwork/java/javase/downloads/index.html) or [Open JDK 8+](http://openjdk.java.net/) (full JDK, JRE is not enough)
+* [Oracle JDK 8+](http://www.oracle.com/technetwork/java/javase/downloads/index.html) or [Open JDK 8+](http://openjdk.java.net/) \(full JDK, JRE is not enough\)
 * [sbt](http://www.scala-sbt.org/)
 * [PostgreSQL 10](https://www.postgresql.org/)
 * [node.js 9+](http://nodejs.org/download/)
 * [yarn package manager](https://yarnpkg.com/)
 * [git](http://git-scm.com/downloads)
 
-### OS X
-If you are using OS X try using this awesome installer:
-https://gist.github.com/normanrz/9128496
+#### OS X
+
+If you are using OS X try using this awesome installer: [https://gist.github.com/normanrz/9128496](https://gist.github.com/normanrz/9128496)
 
 Or install Java manually and run:
 
@@ -79,8 +78,7 @@ psql -c "GRANT ALL PRIVILEGES ON DATABASE webknossos TO postgres;"
 git clone [email protected]:scalableminds/webknossos.git
 ```
 
-
-### Ubuntu 16.04 LTS
+#### Ubuntu 16.04 LTS
 
 ```bash
 # Adding repositories for sbt, nodejs and yarn
@@ -102,48 +100,54 @@ 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
+#### Manual Installation
+
+**Java**
 
-##### Java
-* Install Java JDK 8 (from Oracle or OpenJDK)
+* 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
+**sbt**
+
+See: [http://www.scala-sbt.org/release/docs/Getting-Started/Setup.html](http://www.scala-sbt.org/release/docs/Getting-Started/Setup.html)
 
-##### PostgreSQL
-* Install PostgreSQL from https://www.postgresql.org/download/
+**PostgreSQL**
+
+* Install PostgreSQL from [https://www.postgresql.org/download/](https://www.postgresql.org/download/)
 * PostgreSQL version **10+ is required**
 
-##### node.js & yarn
-* Install node from http://nodejs.org/download/
+**node.js & yarn**
+
+* Install node from [http://nodejs.org/download/](http://nodejs.org/download/)
 * node version **9+ is required**
 * Install yarn package manager: `npm install -g yarn`
 
-### Run locally
+#### Run locally
+
 ```bash
 sbt run
 ```
-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 sbt.
 
-### Run on a remote machine
+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 sbt.
+
+#### Run on a remote machine
+
 ```bash
 sbt "run -Dhttp.uri=http://<remote address>:9000"
 ```
-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 sbt.
 
-Make sure to open port `9000` in your firewall. 
-This is only recommended for development purposes. 
-See below for a recommended production setup.
+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 sbt.
+
+Make sure to open port `9000` in your firewall. This is only recommended for development purposes. See below for a recommended production setup.
+
+### Production setup
 
-## Production setup
 [See wiki](https://github.com/scalableminds/webknossos/wiki/Production-setup) for recommended production setup.
 
-For upgrades, please check the [changelog](CHANGELOG.md) & [migration guide](MIGRATIONS.md).
+For upgrades, please check the [changelog](https://github.com/scalableminds/webknossos/tree/9e11025fdb666afc39298d8b85c5e0a461a20efe/CHANGELOG.md) & [migration guide](https://github.com/scalableminds/webknossos/tree/9e11025fdb666afc39298d8b85c5e0a461a20efe/MIGRATIONS.md).
+
+### Tests
 
-## Tests
 ```bash
 # Frontend linting
 yarn run lint
@@ -161,20 +165,25 @@ yarn test-verbose
 docker-compose run e2e-tests
 ```
 
+### Contact and support
 
-## Contact and support
 Contact us at [[email protected]](mailto:[email protected]).
 
 [scalable minds](https://scalableminds.com) 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/
+### Credits
+
+* scalable minds - [https://scalableminds.com/](https://scalableminds.com/)
+* Max Planck Institute for Brain Research – [https://brain.mpg.de/](https://brain.mpg.de/)
+
+#### Thanks
 
-### Thanks
 * [CircleCI](https://circleci.com/gh/scalableminds/webknossos) for letting us run builds and tests on their CI
 * [Browser Stack](https://www.browserstack.com/) for letting us test WebKnossos on a variety of different devices  
-<a href="https://www.browserstack.com/"><img src="https://p14.zdusercontent.com/attachment/1015988/wustfygoUpQ0faC7tIiaOpJUM?token=eyJhbGciOiJkaXIiLCJlbmMiOiJBMTI4Q0JDLUhTMjU2In0..TpDEVjDPeSTDWdmL0pu6Mw.pdawodFlbAuP4ZbKn5Ucpyq69pCh3bUXv_XH_yJk7CdAzi6IIi7Az6VWriflXVKOyTWtqA8JkxqPu11s9R56jC2I5JwCc1DJILtD_j9fT4rAIth-hvnST0eA_LqBdXpRYKMHtxookA-dZ9pbvHBTFb-JG2PEKl1IXZCw5GlIRgW2Oxieg9xXtFpBN7R6_Q5yRiwuviemrK0ide1ygC8HTMDgdgdbCLuhHDDeNyluU7tR9kVtV7KZDsVd2WIBId-fSyzInofDhlk196_fHwR0WQd1pN7GDVIdfRhxTTTNWTw.g0PCM6T1kBG7AtBwKZmfzQ" width=100 alt="Browserstack Logo"></a>
 
-# License
+  [![Browserstack Logo](https://p14.zdusercontent.com/attachment/1015988/wustfygoUpQ0faC7tIiaOpJUM?token=eyJhbGciOiJkaXIiLCJlbmMiOiJBMTI4Q0JDLUhTMjU2In0..TpDEVjDPeSTDWdmL0pu6Mw.pdawodFlbAuP4ZbKn5Ucpyq69pCh3bUXv_XH_yJk7CdAzi6IIi7Az6VWriflXVKOyTWtqA8JkxqPu11s9R56jC2I5JwCc1DJILtD_j9fT4rAIth-hvnST0eA_LqBdXpRYKMHtxookA-dZ9pbvHBTFb-JG2PEKl1IXZCw5GlIRgW2Oxieg9xXtFpBN7R6_Q5yRiwuviemrK0ide1ygC8HTMDgdgdbCLuhHDDeNyluU7tR9kVtV7KZDsVd2WIBId-fSyzInofDhlk196_fHwR0WQd1pN7GDVIdfRhxTTTNWTw.g0PCM6T1kBG7AtBwKZmfzQ)](https://www.browserstack.com/)
+
+## License
+
 AGPLv3
+