Cross Platform GUI

We now recommend a Registration GUI that is distributed as a plugin for Fiji (see below for details of the Classic MacOSX GUI). Currently this provides a simple way to install CMTK, select input images and registration parameters and construct appropriate registration scripts. However it does not actually run the final registration script - you still have to go to your operating system and run the script directly.



  • Firstly ensure you have your folder structure set-up correctly. This is described in outline below. If you have trouble following any of the steps then please consult this detailed README distributed with the classic MacOSX GUI (formerly available at

  • You will need:
    1. a folder called e.g. yourregistrationfolder then within this folder
    2. a folder for the image stacks to be registered images, where each image should be named as follows

      The important bit here is the presence of 01.nrrd 02.nrrd etc at the end of the file to ensure that the script can identify which channel is which. By default channel 1 will be used for the registration and up to 3 channels will be reformatted.

    3. a folder containing your reference brain refbrain e.g. jfrc2.nrrd
  • Run in Fiji via Plugins –> CMTK Registration –> CMTK Registration GUI

  • Drag and drop requested files/folders onto the that appear
    • You want to drag and drop the folder containing the images to be processed ~/yourregistrationfolder/images into the Input Image or Image Directory dialogue box, note the Registation Folder dialogue box automatically populates as ~/yourregistrationfolder.
    • You want to drag and drop ~/yourregistrationfolder/refbrain/refbrain.nrrd into the Reference Brain dialogue box

  • Ensure the Registration Params are set to Cachero, Ostrovsky 2010

  • Action should be set to Write Script

  • Select how many cores of your computers processor you would like to dedicate to the registration (the plugin automatically selects half the total number of cores available to it).
  • Hit OK - this creates a small script in ~/yourregistrationfolder/commands
  • Navigate to the ~/yourregistrationfolder/commands folder, you will find a new file called munger_<todays date>_<time file created>.command, double click this to run the registration


  • This is a jython script for fiji and in theory should run on all platforms that fiji supports. We have tested it on mac and it should run without any trouble on linux. I am not so sure about Windows, though there is not fundamental reason why it cannot be made to work.

Sample Data

  • 176 Mb test image data set available here

Classic MacOSX GUI

For some time we have provided a simple MacOSX only registration GUI formerly available at

This is being distributed via the zenodo website. The latest version is always accessible using the All released versions are saved on zenodo and can be referred to via their own unique DOIs.

Unzip and put this somewhere sensible e.g. /Applications/ on a Mac. Then read the Readme (carefully) to learn how to prepare your images and start the registration. For the input images you will need to pay particular attention to file names.

You will likely also need to install a copy of Fiji/ImageJ to save your images in the preferred input format (nrrd) and then read the output (also in nrrd).

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