Issues with conversion from .tif multichannel zstack to .nrrd

Hi, I need to export my (originally acquired on a Bruker 2-photon microscope) multichannel .tif zstacks in .nrrd format but the exported file is not preserving the file structure. The saved .nrrd contains the different channel slices in an interleaved (sequential) fashion.

Is there any other path to achieve this conversion to any other medical imaging format (e.g. DICOM) while preserving the file structure? I would like to import my data into 3Dslicer or simple elastix to perform non rigid registration of my volumes but they lack any support for BioFormats.

I uploaded a small tif substack and its nrrd conversion result.
nrrdconversion.zip (6.9 MB)

I dont know much about 3dslicer but it seems as though TIFF is supported (https://www.slicer.org/wiki/Documentation/4.10/SlicerApplication/SupportedDataFormat), do you definitely need to convert the files?

@DS4242

If what you’re doing is using your multi-channel images as a moving or target for registration, I think elastix expects multiple channels to be in separate files. If that’s right, then you could write two nrrds for each multi-channel tif.

John

I would ideally avoid having to split my zstacks (4channels each) since it would complicate my workflow quite a bit, but if I understood correctly I would need to split my stacks in 4 channels and save each one in a separate nrrd. At that point, I could then use a reference channel in elastix to perform the registration and apply the transforms to the remaining channels.

Is that your suggested workflow?

The TIFF importer in 3D slicer is unable to import any metadata or correctly interpret the file structure (or at least I haven’t figured how to do it), my zstacks are imported as a single volume with interleaved channel slices…