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Supported medical image formats#

Note

You can check your currently supported image formats by grabbing the source code from Github and running python3 tests/support.py.

MedPy relies on SimpleITK, which enables the power of ITK for image loading and saving. The supported image file formats should include at least the following.

Medical formats:

  • ITK MetaImage (.mha/.raw, .mhd)

  • Neuroimaging Informatics Technology Initiative (NIfTI) (.nia, .nii, .nii.gz, .hdr, .img, .img.gz)

  • Analyze (plain, SPM99, SPM2) (.hdr/.img, .img.gz)

  • Digital Imaging and Communications in Medicine (DICOM) (.dcm, .dicom)

  • Digital Imaging and Communications in Medicine (DICOM) series (<directory>/)

  • Nearly Raw Raster Data (Nrrd) (.nrrd, .nhdr)

  • Medical Imaging NetCDF (MINC) (.mnc, .MNC)

  • Guys Image Processing Lab (GIPL) (.gipl, .gipl.gz)

Microscopy formats:

  • Medical Research Council (MRC) (.mrc, .rec)

  • Bio-Rad (.pic, .PIC)

  • LSM (Zeiss) microscopy images (.tif, .TIF, .tiff, .TIFF, .lsm, .LSM)

  • Stimulate / Signal Data (SDT) (.sdt)

Visualization formats:

  • VTK images (.vtk)

Other formats:

  • Portable Network Graphics (PNG) (.png, .PNG)

  • Joint Photographic Experts Group (JPEG) (.jpg, .JPG, .jpeg, .JPEG)

  • Tagged Image File Format (TIFF) (.tif, .TIF, .tiff, .TIFF)

  • Windows bitmap (.bmp, .BMP)

  • Hierarchical Data Format (HDF5) (.h5 , .hdf5 , .he5)

  • MSX-DOS Screen-x (.ge4, .ge5)

For informations about which image formats, dimensionalities and pixel data types your current configuration supports, run python3 tests/support.py > myformats.log.

Further information see https://simpleitk.readthedocs.io .