TiffImageIO z spacing about itk HOT 9 CLOSED

There is no standard way of storing a Z spacing in TIFF but the format allows private tags. For example, MIPAV handles ZResolution and GeoTIFF defines ModelPixelScaleTag.

For DICOM slices, here's an example to preserve metadata:

itk::GDCMImageIO::Pointer gdcmIO = itk::GDCMImageIO::New();
ReaderType::DictionaryRawPointer dict = (*(reader->GetMetaDataDictionaryArray()))[sliceNumber];
gdcmIO->SetMetaDataDictionary(*dict);
writer->SetImageIO(gdcmIO);
writer->UseInputMetaDataDictionaryOff();
writer->SetInput(slice2D);
writer->Update();

from itk.

Some more informations: VTK uses Zeiss 3D TIFF and MeVisLab uses SGI 3D TIFF.

from itk.

There are also a couple ImageJ TIFF private tags which can contain 3D information: https://github.com/imagej/ImageJA/blob/master/src/main/java/ij/io/TiffDecoder.java#L43-L44

I can't seem to find a specification for them right now.

from itk.

I wonder if the OpenSlide ImageIO would be any better? #139

from itk.

Not sure about OpenSlide, they had a discussion about supporting 3D about three years ago (openslide/openslide#166) and the project isn't too active, at least on github (https://github.com/openslide/openslide/graphs/code-frequency).

from itk.

This also happens when writing individual DICOM slices/files from a 3D DICOM volume (it clobbers the SpacingBetweenSlices tag "0018|0088" with value 1.0, even if it was there before and not 1.0). My workaround (rather tedious) is to promote the 2D image slice to a 3D volume with a singleton z dimension and extracting/setting the spacing, direction cosines and origin... and then saving the 3D slice to a DICOM file.

from itk.

P.S. openslide, to my knowledge, does not support writing slides/tiffs. If it did, ITKIOOpenSlide would have supported that ability.

from itk.

More info about these tags in this ITK discourse thread:
https://discourse.itk.org/t/unknown-tags-reading-tiff/1719/2

from itk.

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

from itk.