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. NOTE: Warpy Image Combiner itself can be used independently of Warpy, in this case, the only transformation supported are Affine transforms, which can be sufficient for many use cases.

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](https://c4science.ch/w/warpy/imagecombinerwarpy/) 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. NOTE: Warpy Image Combiner itself can be used independently of Warpy, in this case, the only transformation supported are Affine transforms, which can be sufficient for many use cases.

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](https://c4science.ch/w/warpy/imagecombinerwarpy/) 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. NOTE: Warpy Image Combiner itself can be used independently of Warpy, in this case, the only transformation supported are Affine transforms, which can be sufficient for many use cases.