Cytomine-java-client is an open-source Cytomine client written in Java. This client is a Java wrapper around Cytomine REST API gateway.
The main access point to Cytomine data is its REST API. This client is a JAR file that can be imported in a JVM application (Java, Groovy, ...). It allows to import/export data from Cytomine-Core and Cytomine-IMS using RESTful web services e.g. to generate annotation (spatial) statistics, create regions of interest (e.g. tumor masks), add metadata to images/annotations, apply algorithms on image tiles, ...
See documentation for more details.
- Java 1.7+
- Maven 2+ (only if you need to build a new Jar)
To install official release of Cytomine-java-client, see @cytomine. Follow this guide to install forked version by ULiege.
The java client is available with 2 jars:
cytomine-java-client-*-jar-with-dependencies.jar: A jar with all classes (client and dependencies).cytomine-java-client-*.jar: The jar only contains client classes without dependencies classes. A maven pom.xml is provided.
To download and install manually the package, see manual installation procedure.
To retrieve package using Maven or Gradle, see package repository.
To ease development of new Cytomine software, the Cytomine-java-client package is available in Docker containers:
- cytomineuliege/software-java8-base provides a Java 8 (OpenJDK) environment with client already installed.
- cytomineuliege/software-groovy-base provides a Groovy 2.5 (based on OpenJDK 8) environment with client already installed.
These Docker images are tagged with the Python client version number. Two image variants are given for Java 8 version:
cytomineuliege/software-java8-base:<version>is the defacto image. If you are unsure about what your needs are, you probably want to use this one.cytomineuliege/software-java8-base:<version>-slimis an image that does not contain all the common package contained in the default tag and only contains the minimal packages needed to run Java. If you are working in an environment where only the python image will be deployed and you have space constraints, we recommend to use this one.
See official OpenJDK Docker image for more details.
See detailed usage documentation.
Three parameters are required to connect:
CYTOMINE_URL: The full URL of Cytomine core (e.g. “http://demo.cytomine.be”).PUBLIC_KEY: Your cytomine public key.PRIVATE_KEY: Your cytomine private key.
First, the connection object has to be initialized.
Cytomine cytomine = new Cytomine(CYTOMINE_URL, PUBLIC_KEY, PRIVATE_KEY);
The next sample code should print “Hello {username}” where {username} is replaced by your Cytomine username and print the list of available projects.
import be.cytomine.client.*
import be.cytomine.client.models.*
import be.cytomine.client.collections.*
Cytomine cytomine = new Cytomine(CYTOMINE_URL, PUBLIC_KEY, PRIVATE_KEY);
System.out.println("Hello " + cytomine.getCurrentUser().get("username"));
System.out.println("******* You have access to these projects: *******");
ProjectCollection projects = cytomine.getProjects();
for(int i=0; i<projects.size(); i++) {
Project project = projects.get(i);
System.out.println(project.get("name"));
}
When using our software, we kindly ask you to cite our website url and related publications in all your work (publications, studies, oral presentations,...). In particular, we recommend to cite (Marée et al., Bioinformatics 2016) paper, and to use our logo when appropriate. See our license files for additional details.
- URL: http://www.cytomine.org/
- Logo: Available here
- Scientific paper: Raphaël Marée, Loïc Rollus, Benjamin Stévens, Renaud Hoyoux, Gilles Louppe, Rémy Vandaele, Jean-Michel Begon, Philipp Kainz, Pierre Geurts and Louis Wehenkel. Collaborative analysis of multi-gigapixel imaging data using Cytomine, Bioinformatics, DOI: 10.1093/bioinformatics/btw013, 2016.
Apache 2.0