Installation requirements

Automatic installation with Fiji update sites (optional for ImageJ2 and Fiji distributions)

In Fiji or Image2:

• In Fiji/ImageJ, click on Help > Update....
• Once the ImageJ Updater pops up, click on Manage update sites > Add update site.
• There you can write the name ("deepImageJ") and the URL given (https://sites.imagej.net/DeepImageJ/).
• Click on Close.
• Click on Apply Changes. Then The plugin will then be installed automatically together with its java dependencies WARNING!: If you are using Windows, the previous steps will only let you using Tensorflow models. For PyTorch models, you still need to follow one more step: Visual studio installation.

Manual installation (mandatory when using ImageJ1)

• Download the latest release of deepImageJ at GitHub releases. The ZIP file (deepImageJ.zip) contains all the necessary libraries (JAR files) and deepImageJ_X.X.X.jar.
• Unzip the ZIP file.
• Copy the plugin executable DeepImage_X.X.X.jar in the plugins folder of ImageJ1 / Image2 / Fiji directory.
• The folder Dependencies contains all the Java dependencies (.jar) needed. You can take all the dependencies and drag&drop them directly in ImageJ. Whenever it asks where to store them:
  • If you are in ImageJ1, in ImageJ/plugins/jars.
  • Otherwise, in the jars folder inside ImageJ/Fiji.
• Otherwise, you can directly copy&paste all the dependencies in the locations specified above.

The last step might produce some version conflicts with existing libraries in your local installation. Thus being careful is advised. If there are already other versions of the dependencies inside the jars folder, some conflicts might appear when ImageJ2/Fiji is started, and the plugin might not function correctly.