(NOTE) For questions and issues, please use [forum.image.sc](https://forum.image.sc/) (NOTE) Do you find this workflow useful ? Please [cite us](https://doi.org/10.3389/fcomp.2021.780026)! **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+). 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. **Installation instructions are included in this part of the documentation** * **[Image Combiner Warpy](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). NOTE: Warpy Image Combiner itself can be used independently of Warpy. In this case, only affine transformations are supported, which can be sufficient for many use cases. All code of the Warpy workflow can be found within these repositories: * https://github.com/bigdataviewer/bigdataviewer-playground * https://github.com/BIOP/bigdataviewer-biop-tools * https://github.com/BIOP/bigdataviewer-bioformats * https://github.com/BIOP/qupath-extension-warpy ------- 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/).

(NOTE) For questions and issues, please use [forum.image.sc](https://forum.image.sc/) (NOTE) Do you find this workflow useful ? Please cite us: **[An Open-Source Whole Slide Image Registration Workflow at Cellular Precision Using Fiji, QuPath and Elastix - Frontiers in Computer Science](https://doi.org/10.3389/fcomp.2021.780026)** **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+). 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. **Installation instructions are included in this part of the documentation** * **[Image Combiner Warpy](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). NOTE: Warpy Image Combiner itself can be used independently of Warpy. In this case, only affine transformations are supported, which can be sufficient for many use cases. All code of the Warpy workflow can be found within these repositories: * https://github.com/bigdataviewer/bigdataviewer-playground * https://github.com/BIOP/bigdataviewer-biop-tools * https://github.com/BIOP/bigdataviewer-bioformats * https://github.com/BIOP/qupath-extension-warpy ------- 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/).

(NOTE) For questions and issues, please use [forum.image.sc](https://forum.image.sc/) (NOTE) Do you find this workflow useful ? Please [cite uscite us: **[An Open-Source Whole Slide Image Registration Workflow at Cellular Precision Using Fiji, QuPath and Elastix - Frontiers in Computer Science](https://doi.org/10.3389/fcomp.2021.780026)!** **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+). 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. **Installation instructions are included in this part of the documentation** * **[Image Combiner Warpy](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). NOTE: Warpy Image Combiner itself can be used independently of Warpy. In this case, only affine transformations are supported, which can be sufficient for many use cases. All code of the Warpy workflow can be found within these repositories: * https://github.com/bigdataviewer/bigdataviewer-playground * https://github.com/BIOP/bigdataviewer-biop-tools * https://github.com/BIOP/bigdataviewer-bioformats * https://github.com/BIOP/qupath-extension-warpy ------- 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/).