FAQ: Understanding Image Basics

Image Basics

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How do I save images in a different format?

Since MIPAV supports read and write access in a number of different file formats and can read still others. There are some MIPAV-only features, for example, allowing users to recover particular volumes of interest. MIPAV can save and later restore important data. Not only does MIPAV support a number of medical image data formats, but it also supports some general purpose formats, which are very help in making presentations.

When you save an image after working on it in MIPAV, be sure to type the correct extension at the end of the file name to save the image in the correct format.

Example. If you are saving a DICOM image named Head101, type .dcm or .ima as the extension so that the name of the file is Head101.dcm.

The following tables list the image file types that MIPAV supports. For your convenience, you can search for image file types by either of the following:

Manufacturer or application in [FAQMain.backup.html#1026440 Table 1 on page 23]

File extension in [FAQMain.backup.html#1026811 Table 2 on page 24]

Table 1. Graphics file formats supported by MIPAV listed by manufacturerÂ

Manufacturer or Application	File Extension	Open	Save
Adobe Photoshop	PSD	Yes	Yes
AFNI	BRIK, HEAD	Yes	Yes[#1027438 1]
Analyze	IMG	Yes	Yes
Apple Macintosh PICT	PICT	Yes	Yes
Apple QuickTime	MOV, QT	Yes	Yes
Audio/Video Interleave	AVI	Yes	Yes[#1027706 2]
BIORAD	PIC	Yes	No
Bruker	2dseq	Yes	No
Cheshire	IMC, IMG	Yes	Yes
DICOM 3.0	DCM, IMA	Yes	Yes
FITS	FTS	Yes	Yes
FreeSurfer Image	COR	Yes	No
FreeSurfer Surface	ASC	Yes	No
GE - Genesis 5X and LX	SIG	Yes	No
Graphics Interchange File	GIF	Yes	No
Image Cytometry Standard (ICS)	ICS	Yes	Yes
InterFile	HDR	Yes	Yes
Joint Photographics Experts Group	JFI, JFIF, JPG, JPEG	Yes	Yes
Laser Scanning Microscope (Zeiss)	LSM	Yes	Yes
Medical Image Network Common Data Form (including ROIs)	MNC	Yes	Yes
Medical Research Council	MRC	Yes	Yes
MICRO-CAT	LOG	Yes	Yes
Microsoft Windows Bitmap	BMP, DIB	Yes	Yes
MIPAV Image	XML	Yes	Yes
MIPAV Lookup Table	LUT	Yes	Yes
MIPAV Transformation Matrix	MTX	Yes	Yes
MIPAV Graph	PLT	Yes	Yes
MIPAV Volume of Interest	VOI, XML	Yes	Yes
netCDF and masks	CDF	Yes	Yes
PC Paintbrush	PCX, DCX, PCC	Yes	Yes
Portable Network Graphic	PNG	Yes	Yes
Raw	RAW	Yes	Yes
Siemens - Magnetom Vision	IMA	Yes	Yes
Sun Raster	RS, RAS	Yes	Yes
Tagged Image File Format	TIF, TIFF	Yes	Yes
Truevision Graphics Adapter	ICB, TGA, TPIC, VDA, VST	Yes	Yes
XBitMap	XBM	Yes	Yes
XPixMap	XPM	Yes	Yes
Zeiss-TIFF Topography (LSM 510/LSM 5)	LSM	Yes	No

[#1026474 1]MIPAV does not save extra information with the AFNI file. It only does the "bare minimum." [#1026506 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.

Table 2. Graphics file formats supported by MIPAV listed by file extensionÂ

File extension	Manufacturer or Application	Open	Save
2dseq	Bruker	Yes	No
ASC	FreeSurfer Surface	Yes	No
AVI	Audio/Video Interleave	Yes	Yes[#1028137 1]
BMP	Microsoft Windows Bitmap	Yes	Yes
BRIK	AFNI	Yes	Yes[#1028192 2]
CDF	netCDF and masks	Yes	Yes
COR	FreeSurfer Image	Yes	No
DCM	DICOM 3.0	Yes	Yes
DCX	PC Paintbrush	Yes	Yes
DIB	Microsoft Windows Bitmap	Yes	Yes
FTS	FITS	Yes	Yes
GIF	Graphics Interchange File	Yes	No
HDR	InterFile	Yes	Yes
HEAD	AFNI	Yes	Yes[#1028264 3]
ICB	Truevision Graphics Adapter	Yes	Yes
ICS	Image Cytometry Standard (ICS)	Yes	Yes
IMA	DICOM 3.0	Yes	Yes
IMA	Siemens - Magnetom Vision	Yes	Yes
IMC	Cheshire	Yes	Yes
IMG	Analyze	Yes	Yes
IMG	Cheshire	Yes	Yes
JFI	Joint Photographics Experts Group	Yes	Yes
JFIF	Joint Photographics Experts Group	Yes	Yes
JPEG	Joint Photographics Experts Group	Yes	Yes
JPG	Joint Photographics Experts Group	Yes	Yes
LOG	MICRO-CAT	Yes	Yes
LSM	Laser Scanning Microscope (Zeiss)	Yes	Yes
LSM	Zeiss-TIFF Topography (LSM 510/LSM 5)	Yes	No
LUT	MIPAV Lookup Table	Yes	Yes
MNC	Medical Image Network Common Data Form (including ROIs)	Yes	Yes
MOV	Apple QuickTime	Yes	Yes
MRC	Medical Research Council	Yes	Yes
MTX	MIPAV Transformation Matrix	Yes	Yes
PCX	PC Paintbrush	Yes	Yes
PIC	BIORAD	Yes	No
PICT	Apple Macintosh PICT	Yes	Yes
PLT	MIPAV Graph	Yes	Yes
PNG	Portable Network Graphic	Yes	Yes
PSD	Adobe Photoshop	Yes	Yes
QT	Apple QuickTime	Yes	Yes
RAW	Raw	Yes	Yes
RAS	Sun Raster	Yes	Yes
RS	Sun Raster	Yes	Yes
SIG	GE - Genesis 5X and LX	Yes	No
TGA	Truevision Graphics Adapter	Yes	Yes
TIF	Tagged Image File Format	Yes	Yes
TIFF	Tagged Image File Format	Yes	Yes
TPIC	Truevision Graphics Adapter	Yes	Yes
VDA	Truevision Graphics Adapter	Yes	Yes
VOI	MIPAV volume of interest	Yes	Yes
VST	Truevision Graphics Adapter	Yes	Yes
XBM	XBitMap	Yes	Yes
XML	MIPAV volume of interest	Yes	Yes
XML	MIPAV image	Yes	Yes
XPM	XPixMap	Yes	Yes

[#1026853 1]AVIs are saved with encoding options: run-length, MPEG, MPEG-4, QuickTime. However, MIPAV requires the Java Media Framework, which is installed with MIPAV. [#1026869 2]MIPAV does not save extra information with the AFNI file. It only does the "bare minimum." [#1026941 3]MIPAV does not save extra information with the AFNI file. It only does the "bare minimum."

[FAQMain.backup.html#998290 File:FAQMain.backup14.gif ][FAQMain.backup.html#998290 Back to Questions]

How do I combine two images for alphablending?

Alphablending is a technique that adds transparency information to translucent objects. When two images share a window, you can adjust the alphablending settings so that you can see a blend of both images and can compare overlapping regions in two datasets.

To use the alphablending function

1 Open one or more images.

2 Click the image you want to make the active image.

3 Click File > Load, and then click one of the following (refer to [FAQMain.backup.html#1041487 Figure 20]):

Image(B) from Frame-To load an already opened image

Image(B) from File-To load an image from an image file

Multifile(B)-To load more than one image

Blank image(B)-To load a blank image

Figure 20. File > Load menu

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