Image formats descriptions
Contents
- 1 Other formats supported by MIPAV
- 1.1 Adobe Photoshop (PSD) files
- 1.2 Analyze files
- 1.3 AFNI
- 1.4 Audio Video Interleave (AVI) files
- 1.5 BIORAD
- 1.6 Bruker data format
- 1.7 Cheschire (IMG or IMC)
- 1.8 Digital Imaging and Communications in Medicine (DICOM) files
- 1.9 FITS
- 1.10 FreeSurfer image and surface files
- 1.11 GE - Genesis 5X and LX
- 1.12 Graphics Interchange Format (GIF) files
- 1.13 ICS (Image Cytometry Standard)
- 1.14 Joint Photographic Experts Group (JPEG/JFIF) files
- 1.15 Laser Scanning Microscope (Zeiss)
- 1.16 Legacy VTK
- 1.17 LIFF
- 1.18 Macintosh PICT
- 1.19 Medical Image NetCDF (MINC) files
- 1.20 Medical Research Council (MRC)
- 1.21 MICRO-CAT
- 1.22 Microsoft Windows Bitmap (BMP) files
- 1.23 MIPAV (LUT) files
- 1.24 MIPAV (MTX) files
- 1.25 MIPAV (PLT) files
- 1.26 MIPAV text file format
- 1.27 MIPAV (SUR) files
- 1.28 MIPAV (VOI) files
- 1.29 MIPAV XML
- 1.30 MIPAV XML surface format
- 1.31 NIFTI
- 1.32 PC Paintbrush (PCX) files
- 1.33 PICT files
- 1.34 Phillips PAR/REC
- 1.35 POLY
- 1.36 Polygon File Format
- 1.37 Portable Network Graphic Format (PNG) files
- 1.38 QuickTime-Apple
- 1.39 Raw data files
- 1.40 Siemens - Magnetom Vision
- 1.41 STL (ASCII and Binary)
- 1.42 Sun Raster (RS) files
- 1.43 Tag Image File Format (TIFF) files
- 1.44 TARGA
- 1.45 Truevision Graphics Adapter (TGA) files
- 1.46 VRML
- 1.47 VTK XML surface
- 1.48 X BitMap (XBM) files
- 1.49 XML
- 1.50 XML surface
- 1.51 X PixMap (XPM) files
Other formats supported by MIPAV
Adobe Photoshop (PSD) files
Analyze files
Analyze images are formed from two files:
These files have the same name and are distinguished by the extensions HDR for the header file and IMG for image file. For example, brain.hdr is the header file that describes the image file and brain.img is the file that contains the image data. In support of some NIH intramural researchers who have used Analyze in the past and have generated a large number of legacy datasets, MIPAV reads and writes Analyze formatted images. See also [MIPAV_AppCSupportedFormats.html#1254429 "Analyze filesets" on page 606].
AFNI
The HEAD file for an AFNI dataset is in ASCII, so you can view it with a normal text editor (e.g., Notepad). The data within are organized into attributes, which are named arrays of floats, integers, or characters (strings). A sample float attribute is shown in [MIPAV_AppCSupportedFormats.html#1331066 Table 2]. This array defines the voxel array dimensions. An example of a character array attribute is shown in [MIPAV_AppCSupportedFormats.html#1331242 Table 3].
type = integer-attribute name = DATASET_DIMENSIONS count = 5 256 256 124 0 0
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type = string-attribute name = IDCODE_DATE count = 25 'Mon Apr 15 13:08:36 1996~
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Note that the data for a string attribute starts with a single apostrophe (') character, and that the number of bytes is given by the count parameter. The ASCII NUL character is replaced by the tilde ~ so that the HEAD file can be edited manually, if need be. On input, tildes will be replaced with NULs.
The dataset reading code requires a minimal set of attributes to be able to decipher a dataset; for example, the DATASET_DIMENSIONS attribute above is required. There are also some attributes that are not mandatory for a dataset to be successfully constructed from a HEAD file; for example, the IDCODE_DATE attribute above is not required. Attributes that AFNI doesn't know how to deal with are ignored. This makes it possible for a program to tuck extra information into the HEAD file and not cause a trouble.
A BRIK file contains nothing but voxel values. If a dataset has 1 sub-brick, which is 100x100x100 voxels, and the values stored are shorts (2 bytes each), then the BRIK file will have exactly 2,000,000 bytes. All the formatting information is stored in the HEAD file.
Audio Video Interleave (AVI) files
BIORAD
Bruker data format
Bruker format stores a single scanning session in its own directory. The directory is named according to the subject name or number, as typed in by the scanner operator. The directory name usually specifies the subject name/number and which session this is for that subject. For more information, refer to <http://imaging.mrc-cbu.cam.ac.uk/imaging/FormatBruker>.
Cheschire (IMG or IMC)
Digital Imaging and Communications in Medicine (DICOM) files
FITS
FreeSurfer image and surface files
GE - Genesis 5X and LX
Graphics Interchange Format (GIF) files
ICS (Image Cytometry Standard)
The Image Cytometry Standard (ICS) is a digital multidimensional image file format used in life sciences microscopy. It stores the image data and the microscopic parameters describing the optics during the acquisition. The newest ICS2 file format uses a single ICS file with both the header and the data together.
The ICS format is capable to store:
For more information, refer to <http://en.wikipedia.org/wiki/Image_Cytometry_Standard>.
Joint Photographic Experts Group (JPEG/JFIF) files
Laser Scanning Microscope (Zeiss)
Legacy VTK
LIFF
Layered Image File Format is a file format used in the Openlab suite for microscope image processing. It is a proprietary format, but has an open, extensible form analogous to TIFF. It was specifically designed to contain a large number of high resolution images, and also all of the meta data generated by analysis of such images.
Macintosh PICT
Medical Image NetCDF (MINC) files
Medical Research Council (MRC)
MICRO-CAT
Microsoft Windows Bitmap (BMP) files
Depending on the version of BMP, for OS/2 the maximum image size is larger, 64K x 64K or 4G x 4G pixels or voxels. There are several versions of BMP for Microsoft Windows and OS/2. MIPAV supports Microsoft Window BMP versions 2.x and above and all OS/2 versions of the BMP file format. BMP version 2.x is designed for use with the Microsoft Windows 2.x platform. It has a 14-byte header (as does the OS/2 1.x bitmap header). It can accommodate images with 1-, 4-, 8-, or 24-bit colors. Version 3.x is designed for use with the Microsoft Windows 3.x and Windows NT platforms. Like version 2.x, it contains a 14-byte header. It also contains an additional bitmap header that is 40 bytes in size. The Microsoft Windows 3.x platform version accommodates images with 1-, 4-, 8- or 24-bit colors. Windows NT and Windows XP accommodate 16- and 32-bit images. Version 4.x was designed for use with Microsoft Windows 95. It contains the 14-byte header, and an additional 108-byte bitmap header. It can accommodate images of 1, 4, 8, 16, and 32 bits.
MIPAV (LUT) files
MIPAV (MTX) files
MIPAV (PLT) files
MIPAV text file format
MIPAV (SUR) files
MIPAV (VOI) files
MIPAV XML
Refer to [MIPAV_AppCSupportedFormats.html#1260832 "MIPAV XML" on page 571].
MIPAV XML surface format
NIFTI
For more information, refer to the NIfTI web site at <http://nifti.nimh.nih.gov/>.
PC Paintbrush (PCX) files
PICT files
Phillips PAR/REC
and MIPAV User Guide, Volume 2, Algorithms "DTI Create List File".
POLY
Below, is the description of POLY format originally written in 1993 by Pat Flynn and revised 1/96 PJF. For more information refer to:
Each vertex appears on its own line.
The format is `pnt %d: %f %f %f'.
Points are numbered starting at zero. There is no sentinel indicating the end of the points and the beginning of the polygons; your program logic can easily detect it.
Each polygon appears on its own line.
The format is `poly %d: [%d] %d %d %d .... ' The number on the left of the colon is the index of the polygon (numbered from zero). The number inside the [square brackets] is the number of vertices. The remaining numbers are the indices of the vertices. The vertices proceed clockwise around the polygon as you look at it from `outside' the object.
The surface list allows to logically group polygons.
The format for a surface entry is:
Polygon File Format
format ascii 1.0 { ascii/binary, format version number } comment made by Greg Turk { comments keyword specified, like all lines } element vertex 8 { define "vertex" element, 8 of them in file } property float x { vertex contains float "x" coordinate } property float y { y coordinate is also a vertex property } property float z { z coordinate, too } element face 6 { there are 6 "face" elements in the file } property list uchar int vertex_index { "vertex_indices" is a list of ints } end_header { delimits the end of the header } 0 0 0 { start of vertex list } 0 0 1 0 1 1 0 1 0 1 0 0 1 0 1 1 1 1 1 1 0 3 1 2 3 { start of face list } 3 6 5 4 3 4 5 1 3 5 6 2 3 6 7 3 3 7 4 0
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Portable Network Graphic Format (PNG) files
QuickTime-Apple
Raw data files
Siemens - Magnetom Vision
Refer to <http://www.dclunie.com/medical-image-faq/html/part4.html#MagnetomVision>.
STL (ASCII and Binary)
Sun Raster (RS) files
Tag Image File Format (TIFF) files
TARGA
Truevision Graphics Adapter (TGA) files
VRML
VTK XML surface
X BitMap (XBM) files
XML
MIPAV has it's own XML version - MIPAV XML, which is explained in Section [MIPAV_AppCSupportedFormats.html#1260832 "MIPAV XML" on page 571].
XML surface
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