FAQ: Understanding 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, make 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.

For more information about file and image formats supported by MIPAV see also: Opening and loading image files and Image formats descriptions.

Image files supported by MIPAV

The following tables list the image file types that MIPAV supports. See also: Supported Formats and Image formats descriptions.

For your convenience, you can search for image file types by either manufacturer or file extension.

Listed by manufacturer

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

Manufacturer or Application
File Extension
Open
Save
Adobe Photoshop
PSD
Yes
Yes
AFNI
BRIK, HEAD
Yes
Yes[1]
Analyze
IMG
Yes
Yes
Apple Macintosh PICT
PICT
Yes
Yes
Apple QuickTime
MOV, QT
Yes
Yes
Audio/Video Interleave
AVI
Yes
Yes[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
[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.

Listed by file extension

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

File extension
Manufacturer or Application
Open
Save
2dseq
Bruker
Yes
No
ASC
FreeSurfer Surface
Yes
No
AVI
Audio/Video Interleave
Yes
Yes[1]
BMP
Microsoft Windows Bitmap
Yes
Yes
BRIK
AFNI
Yes
Yes[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[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
[ 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.
[ 2]MIPAV does not save extra information with the AFNI file. It only does the "bare minimum."
[3]MIPAV does not save extra information with the AFNI file. It only does the "bare minimum."

What is Image A and Image B?

In MIPAV, the first image opened in an image window is referred to as Image A. When you load, or import, a second image in the same window, MIPAV refers to the second image as Image B.

Note: The abbreviations (A) or (B) appear after some commands. (A), which is the abbreviation for "Image A," indicates that the option is applied to the first image opened in an image window. (B), which is the abbreviation for "Image B," indicates that the option is applied to second image loaded in the image window. For example, if you select Close Image (B), MIPAV closes the second image (Image B) that was loaded in the image window.

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. See also Comparing images using alphablending and Opening and loading image files.

Opening Image A and Image B. Alphablending slider

To use the alphablending function you need to open two or more images. In order to do that:

  1. Click the image you want to make an active image.
  2. Click File > Load, and then click one of the following:
    • 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.
  3. The MIPAV window expands to include the Active Image and Alphablending slider, and the active image window contains all the images selected.
  4. Adjust the alphablending slider at the bottom of the MIPAV window to reveal all of the images.
  5. Move the slider to select the best ratio for the datasets of interest.
  6. Note: The level of translucency for one image is inversely proportional to the other. Thus, if image A is 75 percent transparent (25 percent opaque), then image B is 75 percent opaque (25 percent transparent).

See also:

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