[Insight-users] Problems with SCIFIO

[Sami Koho]

Hello,

I have been having some problems with reading my image data with ITK. My
images are microscope images, originally from a Leica confocal, saved as 3D
tiff volumes in ImageJ. When I open such a file with ITK (version 4.5), I
get a complaint about unknown tags and lose all my metadata (such as voxel
size information). SImilarly. when I save a tiff file with ITK, I seem to
lose all the metadata - at least ImageJ does not understand it.

I ended up installing MetaImage plugin to ImageJ, allowing me to export to
mhd format, which seems to work, for reading data into my ITK application
at least. I still have problems showing the results in ImageJ, as the voxel
sizes go wrong on save.

Last night I compiled ITK with SCIFIO module enabled, as I thought that
this would make handling microscope images a bit more easy. Everything
compiled nicely, but now I get a following error:

python rescaling_test.py psf_red.tif
Traceback (most recent call last):
  File "rescaling_test.py", line 18, in <module>
    image = itkio.itk_read_image(image_path)
  File
"/usr/local/lib/python2.7/dist-packages/iocbio/io/itk_io_utilites.py", line
18, in itk_read_image
    itk_image_reader = getattr(itk.ImageFileReader, image_type).New()
  File "/usr/local/lib/ITK-4.5/Python/itkLazy.py", line 37, in
__getattribute__
    itkBase.LoadModule(module, namespace)
  File "/usr/local/lib/ITK-4.5/Python/itkBase.py", line 95, in LoadModule
    LoadModule(dep, namespace)
  File "/usr/local/lib/ITK-4.5/Python/itkBase.py", line 103, in LoadModule
    if not swigModuleName in sys.modules: module =
loader.load(swigModuleName)
  File "/usr/local/lib/ITK-4.5/Python/itkBase.py", line 214, in load
    return imp.load_module(name, fp, pathname, description)
  File "/usr/local/lib/ITK-4.5/Python/ITKCommonPython.py", line 30, in
<module>
    _ITKCommonPython = swig_import_helper()
  File "/usr/local/lib/ITK-4.5/Python/ITKCommonPython.py", line 26, in
swig_import_helper
    _mod = imp.load_module('_ITKCommonPython', fp, pathname, description)
*ImportError: libitkSCIFIO-4.5.so.1: cannot open shared object file: No
such file or directory*

I am using ITK on 64bit Debian Wheezy (with Python wrapping). I checked,
and there is a file called  libitkSCIFIO-4.5.so.1 in /usr/local/lib. Does
someone have an idea, what is going wrong here?

Best,

Sami
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