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](https://c4science.ch/w/warpy/warpy-extension/) 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](https://fiji.sc/) and analyze their result in [QuPath](https://qupath.github.io/) (v0.3.0). It is designed to register slides that require transformations which are **more complex than affine transform**, by using the [ImgLib2 library](https://imagej.net/libs/imglib2/), [elastix](https://github.com/SuperElastix/elastix), and [BigWarp](https://github.com/saalfeldlab/bigwarp). It consists of two components: * **[Warpy](https://c4science.ch/w/warpy/warpy-extension/)** 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 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, 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[Fiji](https://fiji.sc/) and analyze their result in QuPath[QuPath](https://qupath.github.io/) (v0.3.0). It is especially designed to register slides withthat require transformations which are **more complex than affine transform**, by using the [ImgLib2 library](https://imagej.net/libs/imglib2/), [elastix](https://github.com/SuperElastix/elastix), and [BigWarparp](https://github.com/saalfeldlab/bigwarp). It consists of two components: * * **[Warpy](https://c4science.ch/w/warpy/warpy-extension/)** 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 outputs to generate an on-the-fly computation of the transformed image into the reference one.osite image combining one or several transformed images as a new QuPath Entry (=image). These new QuPath entries can be stored, visualized, New QuPath entries combining several slides can thus be generated exported and analyzed (within a QuPath project 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,. iIn this case, the only transformation supported are Affine transforms, which can be sufficient for many use cases.