ImageCombinerWarpy is a QuPath (v0.3) extension for the non-linear overlay of whole slide images.

It is based on the ImageCombiner.
In addition to the affine transformation used in the ImageCombiner, the ImageCombinerWarpy uses the BIOP Warpy project 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.)

INSTALLATION

ImageCombinerWarpy is included in the BIOP EPFL QuPath Warpy extension.

• Install the latest QuPath version (0.3.1)
• Install the BIOP EPFL QuPath Warpy extension by following its readme
• Restart QuPath

USAGE / APPLICATION

In the QuPath menu you will find the new entry Analyze>ImageCombinerWarpy .

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!)

Open ImageCombinerWarpy and choose an overlay image from your project.

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.

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.)

Use the Brightness&Contrast dialog to select the color channels and display settings of the new image.

Additional Information can be found on https://c4science.ch/w/warpy/imagecombinerwarpy/addinfo/.