From Fiji

Easy Eclipse

Initial setup

You will need to follow the instructions to download and build Fiji from scratch.

Once that is accomplished, just call

bin/eclipse-project-generator.bsh

in the command line. That will generate the projects in the eclipse/ subdirectory from where you can import them into your workspace.

Note: At the time of writing, the project generator does not support submodules. This is just due to lack of time on the author's part, and will likely change once somebody puts enough effort into it.

Importing into your workspace

Open the context menu in the panel on the left side and choose Import... (alternatively, you can click on the File>Import... menu item):

Say that you want to import existing projects in the dialog that pops up:

Now you can deselect the project that you do not want to build:

Voilà: