itk montage tiff without ome-tiff header

Beginner Questions
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1

hello, i use the itk montage stitching tiles and get a tiff file, but it is not standard tiff format i think, which can not be opened in openslide
image
is there a way to get a OME-XML metadata to the tiff file of itk montage output, or any other fomat supported by openslide above
the itk montage has a warning message dealing with an unsuported image format, but its hard to figure out the exact format by the ImageIO name

itk::ImageFileWriterException (000000E7A472EFC0)
Location: "unknown" 
File: D:\projects\ITK\Modules\IO\ImageBase\include\itkImageFileWriter.hxx
Line: 117
Description:  Could not create IO object for writing file F:\projects\ITKMontage\examples\output_micro/montage.ngff
  Tried to create one of the following:
    BMPImageIO
    BioRadImageIO
    Bruker2dseqImageIO
    GDCMImageIO
    GE4ImageIO
    GE5ImageIO
    GiplImageIO
    HDF5ImageIO
    JPEGImageIO
    JPEG2000ImageIO
    LSMImageIO
    MINCImageIO
    MRCImageIO
    MetaImageIO
    NiftiImageIO
    NrrdImageIO
    PNGImageIO
    StimulateImageIO
    TIFFImageIO
    VTKImageIO
  You probably failed to set a file suffix, or
    set the suffix to an unsupported type.
2

No file IO in ITK knows about .ngff file format extension. But ITK can read and write TIFF (probably generic variant) files. Support for ZarrNGFF is a work in progress.

It is possible to add whatever metadata you want to the tiff file of ITK montage output, including OME-XML metadata, but that is not implemented. You are the first person to ask for it, so if you want it you will probably have to implement it yourself.

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3

Could the ITK remote module SCIFIO be helpful here?

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4

Hi,

We should add OME-TIFF metadata input / output support into ITK TIFF’s ImageIO. Tracking issue.

An OME-TIFF could be generated in Python with tifffile with something like:

import itk
import tifffile
import numpy as np

image = itk.imread('montage.mha')
with tifffile.TiffWriter('montage.ome.tif', ometiff=True) as tiff:
    options = dict(photometric='minisblack', tile=(128, 128), compression='zlib')
    axes = 'YX'
    metadata={'axes': axes}
    metadata['PhysicalSizeX'] = image.GetSpacing()[0]
    metadata['PhysicalSizeY'] = image.GetSpacing()[1]
    tiff.write(np.asarray(image), **options, metadata=metadata)

itk.Image Origin and z-spacing could be set with per-Plane: PositionX, PositionY, PositionZ.

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