Slide Set

Batch Processing for ImageJ

Perform reproducible analyses across multiple images and regions.

Save time.

Even simple tasks become complicated when they have to be repeated over many regions in many images. With Slide Set, prepare a task once and automate the repetition.

Stay organized.

Use tables to link images with metadata like group and timepoint information. Save region of interest selections for use in multiple analyses.

Do more.

Use built-in analysis tasks, automate general ImageJ2 plugins, or create custom plugins with a simple API.

Preserve reproducibility.

Avoid error-prone manual repetition without the set-up costs of a scripted solution. Document all analysis configuration parameters and keep results connected to the input data.

More Info

Built with ImageJ2

Slide Set is built with ImageJ2, the next-generation version of the scientific image processor ImageJ. ImageJ2 is still under development, but it's already got lots of cool features. It's also included in Fiji, so there's no need to install it seperately. Find out more about ImageJ2 here.

Getting Started


Slide Set is a plugin for ImageJ, so naturally it requires ImageJ. Specifically, it requires either an up-to-date version of Fiji or the latest release of ImageJ2. Slide Set will not work with plain ImageJ.

The easiest way to use Slide Set is to install it in Fiji using the Fiji updater. It's also possible to install Slide Set manually in Fiji or ImageJ2.

Install with the Fiji Updater

Note: If you don't have the Fiji distribution of ImageJ, you can download it here.

  1. Start Fiji and run the updater (Help > Update Fiji)
  2. Select the Manage Update Sites button at the bottom-left of the updater window
  3. Select Add
  4. Scroll to the bottom of the list of available update sites. For the entry named "New":
    • Change the name field to "Slide Set"
    • Set the URL field to
    • Make sure the box at the left is checked
  5. Select Close
  6. Select Apply Changes
  7. Restart Fiji. Slide Set should appear in the Plugins menu.

And that's it! From now on, running the Fiji updater will also check for Slide Set updates, and install them if they are available.

Things to try if something doesn't work

Install Manually

Slide Set can be installed manually in Fiji or ImageJ2. Simply download the latest version and extract it to the Fiji or ImageJ2 plugins directory. If Slide Set is installed manually, it will not be automatically updated. Slide Set will not work with ImageJ1.

Developed by Benjamin Nanes  |   bnanes  |   @BenjaminNanes  |  |  UT Southwestern

Slide Set would not exist without the many contributors to ImageJ, Fiji, and ImageJ2. Their work is gratefully acknowledged.