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. ------- There is a legacy version of this workflow which was working with QuPath v.0.2.3. [It can be accessed here](https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/wsi_registration_fjii_qupath/).

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

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. ------- There is a legacy version of this workflow which was working with QuPath v.0.2.3.In prevision of c4science retirement, [It can be accessed here](https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/wsi_registration_fjii_qupath/).the documentation of Warpy has been moved to https://imagej.net/plugins/bdv/warpy/warpy