Supported Formats

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Supported formats

This appendix provides information about graphical and file formats used and supported by MIPAV. See also Image File Formats: Past, Present, and Future.

See also: MIPAV configuration files.

Supported graphic and file formats

MIPAV supports three categories of graphic file formats: vector (i.e., volume of interest, or VOI), bitmap (i.e., 2D to 5D grayscale or RGB images), and 3D images.

Graphic formats overview

Vector file formats are usually used to store line-based elements. These elements can be geometric shapes, such as polygons, curves, or splines. The data portion of the vector file contains a mathematical description of elements of an image with specific key points identified. A key point can be thought of as a node or vertex; it marks the place where the line changes direction. For example, a square may contain four key points while a circle may contain many more.

In addition to key points, the vector file usually indicates the line segment's starting point, direction, and length. In MIPAV you can create geometrically shaped contours to indicate VOIs. You can then store the VOIs in a vector formatted file. MIPAV can read and generate several vector-formatted file types including the MIPAV lookup table (LUT), MIPAV MTX, MIPAV Graphics Plot (PLT), and MIPAV VOI files.


Bitmap file formats are usually used to store real-world graphics data - photographs or medical images such as CT scans. The data portion of bitmap files contains numerical data that indicates the color of each pixel or voxel in the image. The bitmap file may also indicate the bit depth, which indicates the number of colors that a pixel or voxel can represent. Typically, the bit depth can be 1, 2, 4, 8, 15, 16, 24, or 32. The number of colors represented is the square of the bit depth. Thus, a 4-bit image can contain 16 colors; an 8-bit image can contain 64 colors; and so on. MIPAV can read and generate a number of bitmap formatted file types, such as Adobe Photoshop (PSD), Graphics Interchange File (GIF), Sun Raster (RS), Tagged Image File Format (TIFF), and Truevision Graphics Adapter (TGA).
MIPAV uses 3D graphic formatted files to store descriptions of the color and shape of 3D models of real-world and imaginary objects.

Supported file formats

To support the wide range of image-processing needs of the NIH intramural research community, MIPAV reads and writes the image file types indicated in Table 1. This table shows the formal name of the file format, the file extensions associated with the format, the numerical format, and whether MIPAV supports the opening and saving of the files in that format.

See also: MIPAV configuration files.

Table 1. Image file formats supported by MIPAV

File format

Extension

Supports

Open

Save

Does not support

AFNI

header HEAD, data BRIK

See AFNI

Y

Y[1]

Analyze

header HDR, data IMG

See also: Analyze files

Y

Y

TBD

Apple Macintosh

PICT

TBD.

Y

Y

ASCII text

TXT

MIPAV defined ascii text surface format. The text surface file records the triangle mesh vertices, normal and connectivity.

Y

Y

Audio Video Interleave

AVI

Uncompressed RLE8

See: Audio Video Interleave (AVI) files

Y

Y[2]

TBD

BFLOAT

BFLOAT

TBD.

Y

Y

Bruker

d3pro, reco, acqp, 2dseq

See Bruker data format

Y

Y

TBD

Cheschire

IMC, IMG

TBD

Y

Y

TBD

Cheschire Overlay

OLY

TBD

Y

N

DICOM 2.0

DCM, IMA

See DICOM files

Y

Y

TBD

DM3

DM3

TBD

FITS

FTS

See also: FITS

Y

Y

TBD

FreeSurfer surface

ASCII, ASC

See also: FreeSurfer image and surface files.

Y

Y

TBD

FreeSurfer image

COR

INFO for the header file and NNN for each slice where NN is the number of the slice. See also: FreeSurfer image and surface files.

Y

Y

TBD

GE - Genesis 5X and LX

SIG

See also: GE - Genesis 5X and LX.

Y

Y

TBD

GE Signa 4.x

GEDNO

See also: GE - Genesis 5X and LX.

Y

N

TBD

Image Cytometry Standard

ICS,

IDS

See Image Cytometry Standard

Y

Y

TBD

Interfile

HDR

TBD

Y

Y

TBD

Laser Scanning Microscope (Zeiss)

LSM

See also: Laser Scanning Microscope (Zeiss) image format.

Y

N

TBD

LIFF

LIFF

See also: LIFF.

TBD

Magnetron Vision

IMA

TBD

Y

Y

MAP

MAP

TBD

Y

N

Medical Image Network Common Data Form (including ROIs)

MNC

See also: Medical Image NetCDF (MINC) files.

Y

Y

TBD

MEDIVISION

BIN

TBD

Y

Y

TBD

MetaMorph Stack

STK

TBD

Y

Y

TBD

Medical Research Council

MRC

See Medical Research Council (MRC)

Y

Y

TBD

MGH/MGZ volume format

MGH,

MGZ

MGH for uncompressed storage; MGZ or.MGH.GZ for compressed storage.

Y

Y

TBD

MICRO-CAT (LOG)

LOG,

CT

See also: MICRO-CAT.

TBD

MINC 1.0, 2.0

MNC

See also: Medical Image NetCDF (MINC) files.

Y

Y

MIPAV-specific file formats

MIPAV LUT

LUT

See also: MIPAV (LUT) files.

MIPAV MTX

MTX

See MIPAV (MTX) files.

MIPAV PLT

PLT

See MIPAV (PLT) files.

MIPAV SUR

SUR

See MIPAV (SUR) files.

MIPAV TXT

TXT

See also: MIPAV TXT files

MIPAV VOI

VOI, XML

See also: MIPAV VOI files

MIPAV XML

XML

Full support, see also: MIPAV VOI in XML and MIPAV XML

N/A

End of MIPAV-specific file formats

MRC

MRC

TBD

Y

Y

Nearly Raw Raster Data (NRRD)

1 file with extension of.NRRD or 2 files with extension of.NHDR for header file and.RAW,.TXT,.HEX,.RAW.GZ, or.RAW.BZ2 for data file

Y

Y

NIFTI

2 files with header HDR and data IMG; or a single file.NII

See "NIFTI"

Y

Y

OSM

WU

TBD

Optical Coherence Tomography

TMG

TBD

Y

Y

Phillips

PAR and PARV2 for header files and REC and FREC for data files

PAR and PARV2 for header files and REC and FREC for data files

See "Phillips PAR/REC"

Y

Y

TBD

PICT

PICT

Encoding of black and white images as bitmap mode PICTs. Encodes grayscale images from 2 to 8-bits as palette mode (PICT format does not have grayscale mode). Encodes palette images as palette mode PICTS, encodes other images as a 24-bit 3 component directed bits PICT.

Decoding of black and white and up to (and including) 32-bit color PICT images. Also supports the decoding of compressed PICT images.

Y

Y

N/A

Polygon File Format or Stanford Triangle Format

PLY

See "Polygon File Format"

Y

Y

QuickTime

QT

See "QuickTime-Apple"

Y

Y

TBD

RAW

RAW

See "Raw data files"

Y

Y

TBD

Siemens CT

Old Siemens Somatom CT format (DR3)

Y

Y

TBD

Siemens - Magnetom Vision

IMA

See "Siemens - Magnetom Vision"

Y

Y

TBD

Siemens MicroCAT

LOG, CT

See also "MICRO-CAT"

Y

Y

SPM

SPM

TBD

Y

Y

STL

STLA, STLB

See also "STL (ASCII and Binary)"

Y

Y

Truevision Graphics Adapter

TGA, VST, VDA, ICB, TPIC

Encodes index color images in an uncompressed TGA palette format; encodes other images in an uncompressed 24-bit TGA format.

Decodes black and white, palette, true color uncompressed images. Decodes 16-bit, 24-bit, and 32-bit true color variants (can include loading of alpha channel).

Y

Y

N/A

Washington University OSM dataset Structure

WU

TBD

Y

Y

TBD

Common raster file formats

Adobe Photoshop

PSD

Encoding of bitmap, grayscale, RGB, and index mode images. Also supports the encoding of RLE compression for all image variants.

Decoding of Adobe Photoshop v 2.5 images (and above) with the following modes: bitmap, grayscale, palette, and RGB.

Y

Y

Alpha saving

BIORAD

PIC

See "BIORAD"

Y

Y

TBD

Graphics Interchange File

GIF

Decoding of interlaced images and images with a transparency information set. See also "Graphics Interchange Format (GIF) files"

Y

N

Encoding of a GIF file

Decoding of multiframe GIFs using the multiframe load mechanism

Joint Photographics Experts Group

JPEG, JPG, JFIF, JFI

See "Joint Photographic Experts Group (JPEG/JFIF) files"

Y

Y

TBD

Microsoft Windows Bitmap

BMP, DIB

Encoding of Index Color Model images as uncompressed BMP palette formats. Other Color Model images are encoded as uncompressed 24-bit BMP formatted files.

Decoding of BMP version 2.x through 4.x files. Also supports the encoding of OS/2 variant files. Supports the encoding of true color and palette images, as well as Run-Length Encoding 8 (RLE8) and RLE4 images. See "Microsoft Windows Bitmap (BMP) files"

Y

Y

Decoding of old versions of BMP files (prior to version 2.x)

Microsoft Windows Cursor

CUR

Y

Y

Microsoft Windows icon

ICO

Y

Y

PC Paintbrush File Format

PCX, DCX, PCC

Encoding of PCX files including uncompressed and RLE-compressed support.

Full support for decoding of PCX files. See PC Paintbrush (PCX) files.

Y

Y

N/A

Portable Network Graphic Format

PNG

Encodes index images as palette PNG images. Also encodes grayscale formatted images (which include grayscale and direct color) with bit masks saved in grayscale file format. Direct color and RGB are encoded as RGB images with an alpha mask (if mask is available from the image). 16-bit depth images are truncated to 8-bit depth when the image is loaded.

Decoding of palette, grayscale, and true color images. Also supports the transparency chunk for palette based images.

Y

Y

Some extension chunks (such as ALPHA)

Sun Raster

RS, RAS

Encodes 8-bit index color images with or without RLE compression or RGB format for other color models.

Decoding of 4, 8, 16, 24, and 32-bit images. Supports the decoding of the old, standard, byte encoded, RGB, TIFF, and IFF format type. See "Sun Raster (RS) files"

Decoding of RAW color map or experimental type images

TARGA

TGA

See also "TARGA"

Y

Y

Tag Image File Format

TIF, TIFF

See also "Tag Image File Format (TIFF) files"

Y

Y

Tiled

X BitMap

XBM

Encoding of 2-color XBM images.

Fully supports the decoding of XBM formatted files.

N/A

X PixMap

XPM

Encoding of XPM palette images.

Fully supports the decoding of XPM formatted files.

Y

Y

Decoding of image files with 3 or more characters per pixel/voxel

End of common raster file formats

Surface description file formats

ASCII text

TXT

Y

Y

ASCII Poly

POLY

See also: POLY

Y

Y

ASCII PLY

PLY

See also "Polygon File Format"

ASCII STL

STL

See also "STL (ASCII and Binary)"

Y

Y

Binary STL

STLB

See also "STL (ASCII and Binary)"

Y

Y

Legacy VTK

VTK

See also: Legacy VT

Y

Y

MIPAV TXT

TXT

See also "MIPAV text file format"

Y

Y

MIPAV surface files

SUR

See also "MIPAV (SUR) files"

Y

Y

VRML

WRL

See also "VRML"

Y

Y

VTK XML

VTP

See also "VTK XML surface"

Y

Y

XML surface

XML

See also "XML surface"

Y

Y

[1]MIPAV does not save extra information with the AFNI file. It only does the "bare minimum."
[2]AVIs are saved with encoding options: run-length, MPEG, MPEG-4, QuickTime. However, MIPAV requires the Java Media Framework, which is installed with MIPAV.

MIPAV XML Format

MIPAV XML is a medical image format used in MIPAV. MIPAV XML provides MIPAV users with a common XML framework that standardizes the creation, processing, and interchange of document metadata across different medical image analysis workflow.
MIPAV XML stores image data in two files - an XML file and *.raw file. The XML file contains a number of image attributes, including items such as file name, ID, number of dimensions, resolution, endianess, orientation, compression, and also the special attribute containing the image pixel data. The *.raw file contains the image data.

MIPAV Image Schema

A MIPAV XML file must be formed according to the MIPAV Image Schema. MIPAV Image Schema and Schema Definition (XSD) are available on the MIPAV web site. For more information, refer to Figure 1 and MIPAV web site http://mipav.cit.nih.gov/development.php

MIPAV Image Schema can also be found here: at image.xsd

MIPAVXML Schema.jpg

Advantages of MIPAV XML format

MIPAV XML can not only be used to describe the image as a whole, e.g. file name, dimensionality, subject information, scan attributes, modality, resolution, etc., but it also stores the image pixel information, VOIs, LUTs, surfaces, and Talairach info associated with the image, as well as tags defining structural divisions of the image.
This architecture makes it feasible to save as much as possible image information in a simple format that can be viewed and edited in any web browser or text editor (e.g. WordPad or Notepad).
It also permits the image created/modified from an original image to retain the metadata associated with its source.
MIPAV allows a user to choose what information should be saved when he/she saves an image to XML format. E.g., when a user saves a DICOM image as XML, the software provides he/she with the dialog box, where one can select which DICOM tags to save to an XML file. This can also be used to anonymize DICOM images.

Description of image formats supported by MIPAV

Refer to Image formats descriptions.

See also: