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Warpy is a workflow that provides a way to register whole slide images in Fiji and analyze their result in QuPath (v0.3+). It is designed to register slides that require 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. Installation instructions are included in this part of the documentation

  • Image Combiner Warpy allows to use Warpy outputs to generate an on-the-fly composite image combining one or several transformed images as a new QuPath Entry (=image). These new QuPath entries can be stored, visualized, exported and analyzed (with caution).

Warpy Image Combiner itself can be used independently of Warpy. In this case, only affine transformations are supported, which can be sufficient for many use cases.

/media/plugins/bdv/warpy/warpy-general-workflow.jpg Workflow overview - The set of images to be registered are all put into a single QuPath project. Registrations are performed in Fiji, images are opened from a QuPath project and each registration result is stored as a file within the Redundant project entry folder. For the analysis, thanks to the registration result found between two images, regions of interest can be transferred in QuPath from one image to another, in order to generate correlated data. It is additionally possible to create a new combined image within QuPath.

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Something’s wrong in this documentation ? Please post your issue or question in the forum.

List of solved issues encountered and reported in the forum:



Source code

The code to perform this workflow is splitted in several parts:

Qupath warpy extension and several repositories for the Fiji side. On the Fiji side, the main components are Bigdataviewer-playground for the management of multiple sources and Bigdataviewer-biop-tools.


There is a legacy version of this workflow which was working with QuPath v.0.2.3. It can be accessed here.