Perform reproducible analyses across multiple images and regions.
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.
Use tables to link images with metadata like group and timepoint information. Save region of interest selections for use in multiple analyses.
Use built-in analysis tasks, automate general ImageJ2 plugins, or create custom plugins with a simple API.
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.
Introduction – See how Slide Set helps keep image analyses organized, efficient, and reproducible.
Video – Watch the Slide Set presentation at the 2015 ImageJ User & Developer Conference.
What's New? – Release notes for the latest version of Slide Set.
Documentation – All the details on which buttons to press to create tables, edit regions of interest, and run commands. Plus, the answers to what exactly each of those commands is doing. The documentation can be accessed directly in Slide Set from the
Examples – Step-by step guides to some cool things that Slide Set can do – Working with Slide Set – Linking commands together – Commands with complex outputs – Automating general ImageJ2 plugins – Advanced functions
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.
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.
Help > Update Fiji)
Manage Update Sitesbutton at the bottom-left of the updater window
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
View files of the 'Slide Set' site
Apply changes, and restart Fiji
Program Filesfolder. If it is, the updater may not work properly.
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.