Cytomine Java client

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.be/
• Logo: http://www.cytomine.be/logo/logo.png
• 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. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btw013?ijkey=dQzEgmXVozFRPPf&keytype=ref

Presentation

Cytomine-java-client is an opensource Cytomine client. It is a JAR file that you can import in your JVM application (Java, Groovy, …). You will be able to manage data in a Cytomine instance according to your credentials: manage users, add annotations, upload images,... For more information about Cytomine, go to http://www.cytomine.be

Requirements:

• Java 1.7+
• Maven 2+ (only if you need to build a new Jar)

Binaries: https://github.com/cytomine/cytomine-java-client/releases

Source code: https://github.com/cytomine/cytomine-java-client

See installation instructions here : https://doc.cytomine.org/dev-guide/clients/java/installation

How to build the Java-client

On the project root directory, run this command:

mvn package

This will build the client and produce two jars in the target directory.

How to import the Java-client

Version higher than 2.2.13 are available in the Maven central repository.

Maven

<dependency>
    <groupId>be.cytomine.client</groupId>
    <artifactId>cytomine-java-client</artifactId>
    <version>2.2.13</version>
</dependency>

Gradle

implementation group: 'be.cytomine.client', name: 'cytomine-java-client', version: '2.2.13'

Groovy with Grape

import be.cytomine.client.models.Ontology

@Grab('be.cytomine.client:cytomine-java-client:2.2.13')

Ontology ontology = new Ontology();
...

How to use the Java-client

You need 3 paramters:

• CYTOMINE_URL: The full URL of the Cytomine core (“http://...cytomine.be”).
• PUBLIC_KEY: Your cytomine public key.
• PRIVATE_KEY: Your cytomine private key.

You first need to init the connection object:

Cytomine cytomine = new Cytomine(CYTOMINE_URL, PUBLIC_KEY, PRIVATE_KEY);

Here is a sample code that should print “Hello ” with your Cytomine username and print the list of projects available.

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"));
}