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Opening images

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Kimberly Meechan edited this page Nov 16, 2021 · 1 revision

Images can be opened in the plugin by clicking the command under Plugins > RegistrationTree > Register Bdv Files.

This will open a menu where you can select the xml of your fixed image, the xml of your moving image and an empty temporary directory (this is where temporary files needed for running elastix will be written - you can delete its contents when you're done using the plugin).

Note: these xml files must be for either the BigDataViewer H5 or N5 format. If your images are not in these formats, you can convert them by opening them in imageJ (as you normally would) and running the command under Plugins > BigDataViewer > Export Current Image as XML/HDF5 or Plugins > BigDataViewer > Export Current Image as XML/N5.

Make sure the scale/voxelSize is set properly in these files.

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