ImageCombinerWarpy is a QuPath (v0.3) extension for the non-linear overlay of whole slide images. It is based on the [ImageCombiner](https://forum.image.sc/t/qupath-scripting-4-image-combiner-register-images-and-create-project-entry/50484). In addition to the affine transformation used in the ImageCombiner, the ImageCombinerWarpy uses the [BIOP Warpy project ](https://c4science.ch/w/warpy/warpy-extension/) to combine whole slide image on a cellular resolution (Warpy). Whole slide images aligned with Warpy can be combined to a new QuPath image entry. Multiple images can be selected and overlaid. The only condition is that Warpy transform files exist for all overlay images, and that all overlay images have been transformed to the same base image. (Combinations of affine transformations and Warpy transformations are not possible.) The ImageCombinerWarpy is an experimental tool. Please read the warnings carefully! = INSTALLATION Download and unpack the latest [qupath-extension-imagecombinerwarpy_vxxx.jar](https://github.com/iwbh15/ImageCombinerWarpy_qp_v0.3/releases/download/v0.1.1/qupath-extension-imagecombinerwarpy-0.1.1.jar) file. Drag&Drop the file onto the main QuPath window OR copy the file into your QuPath extensions folder. (Make sure that there are no older ImageCombinerWarpy versions in the extension directory.) Install the BIOP EPFL Warpy package Restart QuPath = USAGE / APPLICATION In the QuPath menu you will find the new entry Analyze>ImageCombinerWarpy . {F22258682, width = 600} open your QuPath project for which you created the Warpy transform. open your fixed/base image in the viewer. Before starting ImageCombinerWarpy, make sure that your base image viewer is selected! (The image used as fixed image in the Warpy procedure MUST be the base image in ImageCombiner!) {F22258700, width = 700} open ImageCombinerWarpy and choose an overlay image from your project. {F22258720, width = 600} Select the overlay image in the image list. In the ‘Warpy Info’ section you should see the ID of the image and - if present in the project data folder - the Warpy transform file. {F22258738, width = 700} Click the ‘Warpy’ command to create the new, permanent project entry with the image overlay. (The Warpy command is ONLY active if Warpy transform file exists for all overlay images.) NOTE: It is possible to combine only certain image channels in the warped image. To do this, adjust the Brightness&Contrast settings as well as the channel selection for all images (base or overlay image) displayed in a separate viewer before using the ‘Warpy’ command. Further information is described in [(•ᴗ•)/ QuPath scripting (#4): Image Combiner (register images and create project entry)](https://forum.image.sc/t/qupath-scripting-4-image-combiner-register-images-and-create-project-entry/50484/7) . {F22258746, width = 700} Use the Brightness&Contrast dialog to select the color channels and display settings of the new image. {F22258760, width = 700} WARNING: The ImageCombinerWarpy is thought as an experimental tool. It is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. I When transformed and overlaid images are created, the original pixel contents of the images are altered ! The pixel difference between the original and transformed image depends not only on the transformation but also on the downsampling used in the current viewer. This must be taken into account in all analysis steps performed on such transformed images. II The Warpy transformation is based on a special TransformingImageServer class provided via a QuPath Extension package. Additionally, the Warpy transformation is based on slide-specific information regarding spatial deformation in Json format. Should the extension or format of the transformation information change in future versions, or should one of these two important components not be present, old projects may no longer load or may not load correctly. It is therefore strongly recommended to save the images created with ImageCombinerWarpy and thus make them independent of the ImageCombinerWarpy extension and the Warpy transformation.

In prevision of c4science retirement, the documentation of Warpy has been moved to https://imagej.net/plugins/bdv/warpy/warpy