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. = Installation == ImageJ / Fiji * Enable the [bigdataviewer-playground](https://imagej.github.io/Bigdataviewer_Playground) update site * For automated registration : install elastix and transformix: ** Download the [latest release of elastix for your OS](https://github.com/SuperElastix/elastix/releases/tag/5.0.1). This tutorial has been tested for elastix 5.0.1 ** Unzip the release ** For windows users, you 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 invite (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: *** In ImageJ/ Fiji, goto {nav Plugins › BIOP › Set and Check Wrappers} then indicate the proper location of required executable files {F18020664} *** This should show up in the ImageJ console : `[INFO] Transformix -> set :-) Elastix -> set :-)` == QuPath Install the latest QuPath 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 archive * put jars in folder TODO When you start QuPath, you should specify the location of your common extension folder. When QuPath is restarted, a BIOP menu should appear on top of the QuPath window. = Usage == Create your QuPath project Create first a QuPath project containing all the slides that you want to register. NOTE : Supported files are the ones which can be opened with the Bio-Formats reader, and which are properly calibrated (the pixels units should be properly specified). If your file format is not supported, you'll need to convert it to a Bio-Formats readable file (TODO : link to convertion options). If you do not have files, here is a demo dataset that you can download for testing : TODO == Registration in Fiji == Analysis in QuPath