Page MenuHomec4science

Warpy - Whole Slide Image (WSI) Registration With ImageJ/Fiji, Elastix and QuPath
Updated 9 Days AgoPublic

WARNING: WORK IN PROGRESS. THIS DOCUMENTED WORKFLOW IS NOT YET RELEASED.
NOTE: For questions and issues, please use forum.image.sc

Warpy is a workflow that provides a way to register whole slide images in Fiji and analyze their result in QuPath (v0.3.0). 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.
  • 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). To use Warpy Image Combiner, you will need to install both Warpy AND Warpy Image Combiner.
NOTE: 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.

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

Last Author
chiarutt
Last Edited
Thu, Nov 25, 09:04

Event Timeline

romainGuiet created this document.Wed, Nov 17, 16:49
romainGuiet edited the content of this document. (Show Details)
romainGuiet added a project: warpy.
romainGuiet changed the visibility from "warpy (Project)" to "Public (No Login Required)".
romainGuiet added a project: Restricted Project.
romainGuiet added subscribers: phaub, chiarutt.
chiarutt edited the content of this document. (Show Details)Wed, Nov 17, 20:21
chiarutt edited the content of this document. (Show Details)
chiarutt edited the content of this document. (Show Details)
chiarutt edited the content of this document. (Show Details)Wed, Nov 17, 20:29
chiarutt published a new version of this document.
chiarutt edited the content of this document. (Show Details)Wed, Nov 17, 20:32
chiarutt edited the content of this document. (Show Details)Wed, Nov 17, 20:57
chiarutt edited the content of this document. (Show Details)
chiarutt changed the title from Warpy to Warpy - Whole Slide Image (WSI) Registration With ImageJ/Fiji, Elastix and QuPath.Wed, Nov 17, 21:04
chiarutt edited the content of this document. (Show Details)Thu, Nov 25, 09:04