WARNING: WORK IN PROGRESS. THIS DOCUMENTED WORKFLOW IS NOT YET RELEASED.

Warpy is a workflow that provides a way to register whole slide images in Fiji and analyze their result in QuPath. It is especially designed to register slides with transformations which are more complex than affine transform, by using the ImgLib2 library, elastix, and BigWarp.

It consists of two components:

• [Warpy]() itself is the component that allows to perform the registration, by using Fiji as an intermediate step. It outputs a transformation which is readable in QuPath and which allows to transfer regions of interest from one image to the registered ones. However, the image itself is not transformed.

• [Warpy Image Combiner]() allows to use the Warpy output to generate an on-the-fly computation of the transformed image into the reference one. New QuPath entries combining several slides can thus be generated within a QuPath project. To use Warpy Image Combiner, you will need to install both Warpy AND Warpy Image Combiner.