We have a template repository to get you started, modified for the BIOP context (essentially specifying the contributors).
You should have git and intellij idea community edition installed. See version-control.
git clone https://github.com/imagej/example-imagej2-command
Then:
Replace the contents of README.md with information about your project.
If you cloned the example-imagej-command repository, you probably want to publish the result in your own repository:
An easy way to find the dependency of a plugin you'd like to depend on in your own plugin is to press Source in the Fije search bar. Even without pressing source you will see the repo coordinates (group, artifact, version) of the plugin you'd like to use.
Trackmate is an IJ1 plugin but it is nicely registered as a maven dependency. So you just need to add its dependency in the pom.xml file:
<dependency>
<groupId>sc.fiji</groupId>
<artifactId>TrackMate_</artifactId>
</dependency>
(try to avoid this... it's going to be a pain in the long term, and immediately for the deployment)
However GDSC_SMLM for instance is neither in maven central nor in scijava maven. Only jars in the update site are accessible. To add IJ1 plugins from this update site in the IDE:
File>Project Structure > Project Settings > Librairies > (+) then add all pre-downloaded jars from the update site, which you would have put into an appropriate folder (path_of_the_jars_of_ij1_update_site).For these plugins to be detected in the IJ1 instance launched from the IDE :
System.setProperty("plugins.dir", "path_of_the_jars_of_ij1_update_site");
final ImageJ ij = new ImageJ();
ij.ui().showUI();
we often use the a simple class to start imagej :
import net.imagej.ImageJ;
// TODO: Consider removing or adding to EasyXT directly as a means of debugging
public class IJSimpleLaunch {
public static void main(String... args) {
ImageJ ij = new ImageJ();
ij.ui().showUI();
}
}