File Formats - 3dct/open_iA GitHub Wiki

open_iA supports several common (image/volume and mesh) file formats. It reads:

  • Raw images (uncompressed binary data)
    • Files with any extension can be opened as raw via dedicated "Open Raw" File menu entry)
    • Some file extensions are automatically detected as raw images: *.pro, *.raw, *.rec, *.vol
    • Parameters can be guessed from the filename:
      • Size: WxHxD (with W, H and D each being integer numbers): Size X = W, Size Y = H, Size Z = D
      • Spacing: Sum / Smm (with S a floating point number, where - can also be used as comma; optionally also 3 entries can be specified separated by x, similar to size); -> Spacing: S in x, y and z direction
      • Data Type: Nbit (with N=8,16,32,64), results in:
        • 8 -> unsigned char (0..255)
        • 16 -> unsigned short (0..65535)
        • 32 -> unsigned int (0..4294967296)
        • 64 -> unsigned long long (0..2^64)
  • MetaImage (*.mhd, *.mha)
  • VG Studio Scenes (*.vgi, *.vgl) - partial support
  • DICOM series (*.dcm)
  • Olympus FluoView files (*.oif)
  • AmiraMesh files (*.am) (only the uncompressed volume data format)
  • Serial VTK Image data (*.vti)
  • Several common image formats (*.bmp, *.jpg/*.jpeg, *.png, *.tiff/*.tif) (plus stacks of such images as volumes)
  • Hierarchical Data Format v5 (HDF5) (*.hdf5, *.he5, *.h5)
  • Matlab (*.mat) files (.mat file format version 7.3, which uses HDF5, see https://mathworks.com/help/matlab/import_export/mat-file-versions.html)
  • STL files (Polygon data) (*.stl)
  • NRRD (*.nrrd)
  • NIFTI (*.nia, *.nii, *.nii.gz)
  • NKC ultrasound data (*.nkc)
  • STL files (*.stl)
  • WaveFront OBJ files (*.obj)

It writes:

  • Volumes:
    • MetaImage, in its bundled .mha format, or the combination of a .mhd descriptor and a .raw file (the latter is a standard raw file, as can be read by most programs dealing with volumes, if additionally given the volume dimensions and spacing, as given in the .mhd descriptor file)
    • Image Stacks (*.bmp, *.jp(e)g, *.png, *.tif(f))
    • AmiraMesh files (only the uncompressed volume data format)
    • File formats supported by ITK (e.g. DICOM, .gipl, NIFTI, NRRD)
    • HDF5
    • VTK XML image data
  • Meshes:
    • STL files
    • WaveFront OBJ files