This page documents a way to register whole slide images in Fiji and analyze their result in QuPath. This workflow allows to register slides with transformations which are more complex than affine transform. Reasonably, if the sample is not too deformed, registration at the cellular level can be achieved on the whole slide area. In this documentation, a demo dataset is used where a fluorescent WSI image is registered to a RGB DAB image. The demo dataset can be [downloaded here](https://perdu.com/). = Installation == ImageJ / Fiji * Enable the [bigdataviewer-playground](https://imagej.github.io/Bigdataviewer_Playground) update site, then restart Fiji. * To enable automated registrations capabilities, install elastix: ** Download the [latest release of elastix for your OS](https://github.com/SuperElastix/elastix/releases/tag/5.0.1). This documentation has been tested for elastix 5.0.1. ** Unzip it ** For windows users, you also need to install [Visual C++ redistributable](https://support.microsoft.com/en-us/topic/the-latest-supported-visual-c-downloads-2647da03-1eea-4433-9aff-95f26a218cc0), you'll most probably need `vc_redist.x64.exe` ** Check, in a command line that elastix can run: *** On windows launch a command console `cmd.exe`, go to the elastix folder, then type `elastix.exe --help`. Check that you got some useful help message and not errors. *** Not tested on mac and linux, but you probably need to type either `elastix --help` or `.\elastix --help` to check proper functioning as well ** Indicate `elastix` and `transformix` executable location in Fiji: *** Execute {nav Plugins › BIOP › Set and Check Wrappers} then indicate the proper location of executable files {F18020664, size=full} *** This should show up in the ImageJ console : `[INFO] Transformix -> set :-) Elastix -> set :-)` == QuPath Install the [latest QuPath version](https://qupath.github.io/) Install the latest release of [QuPath biop extensions](https://github.com/BIOP/qupath-biop-extensions/releases). (TODO make the proper release): * Download the latest release * Extract zip * Put jars in folder TODO When you start QuPath, you should specify the location of your common extension folder: * TODO When QuPath is restarted, a BIOP menu should appear on top of the QuPath window: {F18022329, size=full} = Usage == Create your QuPath project Create first a QuPath project containing all the slides that you want to register. If you do not have files, here is a demo dataset that you can download for testing : TODO, add zenodo link. {F18022361, size=full} WARNING: Only the Bio-Formats image server is supported on the FIJI side. If your image can't be loaded in QuPath using the `Bio-Formats builder`, you can convert your slides in `ome.tiff` format. Several options are available, for instance by using [bfconvert with Kheops](https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/imagej_tools/ijp-kheops/), or [bioformatsf2raw](https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/qupath/ome-tiff-conversion/) for a fast conversion. WARNING: All files need to be properly calibrated (microns, millimeters, etc, but not pixels!). Check on the image tab of QuPath that you have a proper physical unit specified, and not pixels! {F18022412, size=full} Save your project, and your are done for now on the QuPath side. NOTE: You can let QuPath open while performing the registration on Fiji. == Registration in Fiji == Analysis in QuPath