I need to use ITK based image analysis software (i.e. elastix) and need to find a file-format that
- supports 4D images
- can be written from Java
- is opened properly (including pixel size metadata) by ITK (elastix)
So far, for 3D data I have successfully used the MHD file format: https://itk.org/Wiki/ITK/MetaIO/Documentation#Reading_a_Brick-of-Bytes_.28an_N-Dimensional_volume_in_a_single_file.29
However, from ImageJ saving 4D (3D + time) hyperstacks into MHD (using [ File > Save As > MHD ] ) still results in 3D images.
I guess I have two questions:
- Does someone know of a Java implementation of MHD reader and writer that supports 4D? @ctrueden @s.besson
- Does someone know of another suitable 4D image file format that is understood by ITK/elastix? @bogovicj
Thanks a lot for your help!