Difference between revisions of "Technical Information"
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=== Supported file formats === | === Supported file formats === | ||
− | <div style="font-style: normal; font-weight: normal; margin-bottom: 6pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 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 | + | <div style="font-style: normal; font-weight: normal; margin-bottom: 6pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 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.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> . |
{| border="1" cellpadding="5" | {| border="1" cellpadding="5" | ||
− | |+ <div class="TableTitle">Table 1. | + | |+ <div class="TableTitle">Table 1. Image file formats supported by MIPAV </div> |
|- bgcolor="#CCCCCC" | |- bgcolor="#CCCCCC" | ||
! | ! | ||
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header HEAD, data BRIK | header HEAD, data BRIK | ||
| | | | ||
− | See | + | See "AFNI" |
| | | | ||
Y | Y | ||
Line 55: | Line 55: | ||
header HDR, data IMG | header HDR, data IMG | ||
| | | | ||
− | See | + | See "Analyze files" |
| | | | ||
Y | Y | ||
Line 96: | Line 96: | ||
Uncompressed RLE8 | Uncompressed RLE8 | ||
− | See | + | See "Audio Video Interleave (AVI) files" |
| | | | ||
Y | Y | ||
Line 122: | Line 122: | ||
d3pro, reco, acqp, 2dseq | d3pro, reco, acqp, 2dseq | ||
| | | | ||
− | See | + | See "Bruker data format" |
| | | | ||
Y | Y | ||
Line 161: | Line 161: | ||
DCM, IMA | DCM, IMA | ||
| | | | ||
− | See | + | See "Digital Imaging and Communications in Medicine (DICOM) files" |
| | | | ||
Y | Y | ||
Line 187: | Line 187: | ||
FTS | FTS | ||
| | | | ||
− | See | + | See "FITS" |
| | | | ||
Y | Y | ||
Line 200: | Line 200: | ||
[http://wideman-one.com/gw/brain/fs/surfacefileformats.htm ASCII, ASC] | [http://wideman-one.com/gw/brain/fs/surfacefileformats.htm ASCII, ASC] | ||
| | | | ||
− | See | + | See "FreeSurfer image and surface files" |
| | | | ||
Y | Y | ||
Line 226: | Line 226: | ||
SIG | SIG | ||
| | | | ||
− | See | + | See "GE - Genesis 5X and LX" |
| | | | ||
Y | Y | ||
Line 254: | Line 254: | ||
IDS | IDS | ||
| | | | ||
− | See | + | See "ICS (Image Cytometry Standard)" |
| | | | ||
Y | Y | ||
Line 280: | Line 280: | ||
LSM | LSM | ||
| | | | ||
− | See | + | See "Laser Scanning Microscope (Zeiss)" |
| | | | ||
Y | Y | ||
Line 293: | Line 293: | ||
LIFF | LIFF | ||
| | | | ||
− | See | + | See "LIFF" |
| | | | ||
Line 332: | Line 332: | ||
MNC | MNC | ||
| | | | ||
− | See | + | See "Medical Image NetCDF (MINC) files" |
| | | | ||
Y | Y | ||
Line 371: | Line 371: | ||
MRC | MRC | ||
| | | | ||
− | See | + | See "Medical Research Council (MRC)" |
| | | | ||
Y | Y | ||
Line 401: | Line 401: | ||
CT | CT | ||
| | | | ||
− | See | + | See "MICRO-CAT" |
| | | | ||
Line 414: | Line 414: | ||
MNC | MNC | ||
| | | | ||
− | See | + | See "Medical Image NetCDF (MINC) files" |
| | | | ||
Y | Y | ||
Line 430: | Line 430: | ||
LUT | LUT | ||
| | | | ||
− | See | + | See "MIPAV (LUT) files" |
| | | | ||
Line 443: | Line 443: | ||
MTX | MTX | ||
| | | | ||
− | See | + | See "MIPAV (MTX) files" |
| | | | ||
Line 456: | Line 456: | ||
PLT | PLT | ||
| | | | ||
− | See | + | See "MIPAV (PLT) files" |
| | | | ||
Line 469: | Line 469: | ||
SUR | SUR | ||
| | | | ||
− | See | + | See "MIPAV (SUR) files" |
| | | | ||
Line 482: | Line 482: | ||
TXT | TXT | ||
| | | | ||
− | See also | + | See also "MIPAV text file format" |
| | | | ||
Line 495: | Line 495: | ||
VOI, XML | VOI, XML | ||
| | | | ||
− | See [ | + | See ["MIPAV (VOI) files" |
| | | | ||
Line 508: | Line 508: | ||
XML | XML | ||
| | | | ||
− | Full support, see | + | Full support, see "MIPAV XML" |
| | | | ||
Line 548: | Line 548: | ||
2 files with header HDR and data IMG; or a single file.NII | 2 files with header HDR and data IMG; or a single file.NII | ||
| | | | ||
− | See | + | See "NIFTI" |
| | | | ||
Y | Y | ||
Line 589: | Line 589: | ||
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 | + | See "Phillips PAR/REC" |
| | | | ||
Y | Y | ||
Line 617: | Line 617: | ||
PLY | PLY | ||
| | | | ||
− | See | + | See "Polygon File Format" |
| | | | ||
Y | Y | ||
Line 630: | Line 630: | ||
QT | QT | ||
| | | | ||
− | See | + | See "QuickTime-Apple" |
| | | | ||
Y | Y | ||
Line 643: | Line 643: | ||
RAW | RAW | ||
| | | | ||
− | See | + | See "Raw data files" |
| | | | ||
Y | Y | ||
Line 669: | Line 669: | ||
IMA | IMA | ||
| | | | ||
− | See | + | See "Siemens - Magnetom Vision" |
| | | | ||
Y | Y | ||
Line 682: | Line 682: | ||
LOG, CT | LOG, CT | ||
| | | | ||
− | See also | + | See also "MICRO-CAT" |
| | | | ||
Y | Y | ||
Line 708: | Line 708: | ||
STLA, STLB | STLA, STLB | ||
| | | | ||
− | See also | + | See also "STL (ASCII and Binary)" |
| | | | ||
Y | Y | ||
Line 767: | Line 767: | ||
PIC | PIC | ||
| | | | ||
− | See | + | See "BIORAD" |
| | | | ||
Y | Y | ||
Line 780: | Line 780: | ||
GIF | GIF | ||
| | | | ||
− | Decoding of interlaced images and images with a transparency information set. See also | + | Decoding of interlaced images and images with a transparency information set. See also "Graphics Interchange Format (GIF) files" |
| | | | ||
Y | Y | ||
Line 795: | Line 795: | ||
[http://www.scantips.com/basics9j.html JPEG, JPG, JFIF, JFI] | [http://www.scantips.com/basics9j.html JPEG, JPG, JFIF, JFI] | ||
| | | | ||
− | See | + | See "Joint Photographic Experts Group (JPEG/JFIF) files" |
| | | | ||
Y | Y | ||
Line 810: | Line 810: | ||
Encoding of Index Color Model images as uncompressed BMP palette formats. Other Color Model images are encoded as uncompressed 24-bit BMP formatted files. | 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 | + | 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 | ||
Line 847: | Line 847: | ||
Encoding of PCX files including uncompressed and RLE-compressed support. | Encoding of PCX files including uncompressed and RLE-compressed support. | ||
− | Full support for decoding of PCX files. See | + | Full support for decoding of PCX files. See "PC Paintbrush (PCX) files" |
| | | | ||
Y | Y | ||
Line 877: | Line 877: | ||
Encodes 8-bit index color images with or without RLE compression or RGB format for other color models. | 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 | + | 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" |
| | | | ||
Line 890: | Line 890: | ||
TGA | TGA | ||
| | | | ||
− | See also | + | See also "TARGA" |
| | | | ||
Y | Y | ||
Line 903: | Line 903: | ||
TIF, TIFF | TIF, TIFF | ||
| | | | ||
− | See also | + | See also "Tag Image File Format (TIFF) files" |
| | | | ||
Y | Y | ||
Line 965: | Line 965: | ||
POLY | POLY | ||
| | | | ||
− | See also | + | See also "POLY" |
| | | | ||
Y | Y | ||
Line 978: | Line 978: | ||
PLY | PLY | ||
| | | | ||
− | See also | + | See also "Polygon File Format" |
| | | | ||
Line 991: | Line 991: | ||
STL | STL | ||
| | | | ||
− | See also | + | See also "STL (ASCII and Binary)" |
| | | | ||
Y | Y | ||
Line 1,004: | Line 1,004: | ||
STLB | STLB | ||
| | | | ||
− | See also | + | See also "STL (ASCII and Binary)" |
| | | | ||
Y | Y | ||
Line 1,017: | Line 1,017: | ||
VTK | VTK | ||
| | | | ||
− | See also | + | See also "Legacy VTK" |
| | | | ||
Y | Y | ||
Line 1,030: | Line 1,030: | ||
TXT | TXT | ||
| | | | ||
− | See also | + | See also "MIPAV text file format" |
| | | | ||
Y | Y | ||
Line 1,043: | Line 1,043: | ||
SUR | SUR | ||
| | | | ||
− | See also | + | See also "MIPAV (SUR) files" |
| | | | ||
Y | Y | ||
Line 1,056: | Line 1,056: | ||
WRL | WRL | ||
| | | | ||
− | See also | + | See also "VRML" |
| | | | ||
Y | Y | ||
Line 1,069: | Line 1,069: | ||
VTP | VTP | ||
| | | | ||
− | See also | + | See also "VTK XML surface" |
| | | | ||
Y | Y | ||
Line 1,082: | Line 1,082: | ||
XML | XML | ||
| | | | ||
− | See also | + | See also "XML surface" |
| | | | ||
Y | Y | ||
Line 1,093: | Line 1,093: | ||
{| | {| | ||
| | | | ||
− | <div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> [ | + | <div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> [<sup>1</sup>]MIPAV does not save extra information with the AFNI file. It only does the "bare minimum."<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> [#1330214 <sup>2</sup>]AVIs are saved with encoding options: run-length, MPEG, MPEG-4, QuickTime. However, MIPAV requires the Java Media Framework, which is installed with MIPAV.<br /></font></div> |
|} | |} | ||
− | |||
− | |||
=== MIPAV XML === | === MIPAV XML === |
Revision as of 00:23, 16 February 2012
Contents
Supported formats
- "Supported formats"
- "Understanding MIPAV-related files"
- "Other formats supported by MIPAV"
Supported formats
Graphic formats overview
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. See also [MIPAV_AppCSupportedFormats.html#998529 "Understanding MIPAV-related files" on page 594].
Supported file formats
File format |
Extencion |
Supports |
Open |
Save |
Does not support |
---|---|---|---|---|---|
AFNI |
header HEAD, data BRIK |
See "AFNI" |
Y |
Y[#1330166 1] |
|
header HDR, data IMG |
See "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[#1330210 2] |
TBD |
BFLOAT |
BFLOAT |
TBD. |
Y |
Y |
|
d3pro, reco, acqp, 2dseq |
See "Bruker data format" |
Y |
Y |
TBD | |
Cheschire |
IMC, IMG |
TBD |
Y |
Y |
TBD |
Cheschire Overlay |
OLY |
TBD |
Y |
N |
|
DCM, IMA |
See "Digital Imaging and Communications in Medicine (DICOM) files" |
Y |
Y |
TBD | |
DM3 |
DM3 |
TBD |
|||
FTS |
See "FITS" |
Y |
Y |
TBD | |
FreeSurfer surface |
See "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 |
Y |
Y |
TBD |
SIG |
See "GE - Genesis 5X and LX" |
Y |
Y |
TBD | |
GE Signa 4.x |
GEDNO |
TBD |
Y |
N |
TBD |
ICS, IDS |
See "ICS (Image Cytometry Standard)" |
Y |
Y |
TBD | |
HDR |
TBD |
Y |
Y |
TBD | |
Laser Scanning Microscope (Zeiss) |
LSM |
See "Laser Scanning Microscope (Zeiss)" |
Y |
N |
TBD |
LIFF |
LIFF |
See "LIFF" |
TBD | ||
Magnetron Vision |
IMA |
TBD |
Y |
Y |
|
MAP |
MAP |
TBD |
Y |
N |
|
Medical Image Network Common Data Form (including ROIs) |
MNC |
See "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 "MICRO-CAT" |
TBD | ||
MINC 1.0, 2.0 |
MNC |
See "Medical Image NetCDF (MINC) files" |
Y |
Y |
|
MIPAV-specific file formats | |||||
MIPAV LUT |
LUT |
See "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 text file format" |
|||
MIPAV VOI |
VOI, XML |
See ["MIPAV (VOI) files" |
|||
MIPAV XML |
XML |
Full support, see "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 |
|
QT |
See "QuickTime-Apple" |
Y |
Y |
TBD | |
RAW |
See "Raw data files" |
Y |
Y |
TBD | |
Siemens CT |
Old Siemens Somatom CT format (DR3) |
Y |
Y |
TBD | |
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 |
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 |
PIC |
See "BIORAD" |
Y |
Y |
TBD | |
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 |
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 |
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 | |
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 VTK" |
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." [#1330214 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
MIPAV Image Schema
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.
Other formats supported by MIPAV
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