Difference between revisions of "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. | 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, | + | 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 <span style="font-family:courier">Head101</span>, type <span style="font-family:courier">.dcm</span> or <span style="font-family:courier">.ima</span> as the extension so that the name of the file is <span style="font-family:courier">Head101.dcm.</span> | |
− | + | ||
− | + | For more information about file and image formats supported by MIPAV see also: [[Opening and loading image files]] and [[Image formats descriptions]]. | |
− | + | ||
− | + | <div id="FilesExtensions"></div> | |
− | '''Example.'''If you are saving a DICOM image named | + | == 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 [[#ListedManufacturer |manufacturer]] or [[#ListedExtension | file extension]]. | |
− | <div | + | <div id="ListedManufacturer"></div> |
+ | === Listed by manufacturer === | ||
{| border="1" cellpadding="5" | {| border="1" cellpadding="5" | ||
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<div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 18pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -12pt; 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: 30pt; margin-right: 18pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> [<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> | <div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 18pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -12pt; 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: 30pt; margin-right: 18pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> [<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> | ||
|} | |} | ||
+ | |||
+ | <div id="ListedExtension"></div> | ||
+ | === Listed by file extension === | ||
+ | |||
{| border="1" cellpadding="5" | {| border="1" cellpadding="5" | ||
Line 898: | Line 905: | ||
|} | |} | ||
− | == | + | == 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''. <br /> | |
− | + | '''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? == | |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | [http://en.wikipedia.org/wiki/Alpha_compositing 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 [[Changing Image Contrast#ComparingImages | Comparing images using alphablending]] and [[Opening and loading image files]]. | |
− | + | [[File:ImageAImageB.jpg|370px|thumb|left|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: | |
− | | | + | |
− | [[Image | + | <ol> |
− | + | <li>Click the image you want to make [[Opening and loading image files#ActiveImage |an active image]].</li> | |
+ | <li>Click File > Load, and then click one of the following:</li> | ||
+ | <ul> | ||
+ | <li>Image(B) from Frame - To load an already opened image;</li> | ||
+ | <li>Image(B) from File - To load an image from an image file;</li> | ||
+ | <li>Multifile(B) - To load more than one image;</li> | ||
+ | <li>Blank image(B) - To load a blank image.</li> | ||
+ | </ul> | ||
+ | <li>The MIPAV window expands to include the Active Image and Alphablending slider, and the active image window contains all the images selected.</li> | ||
+ | <li>Adjust the alphablending slider at the bottom of the MIPAV window to reveal all of the images.</li> | ||
+ | <li>Move the slider to select the best ratio for the datasets of interest.</li> | ||
+ | '''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).<br /> | ||
+ | </ol> | ||
+ | |||
+ | == See also: == | ||
+ | *[[Getting Started Quickly with MIPAV]] | ||
+ | *[[Opening and loading image files]] | ||
+ | *[[Changing Image Contrast#ComparingImages | Comparing images using alphablending]] | ||
+ | *[[Displaying images]] | ||
+ | *[[Supported Formats]] | ||
+ | *[[Image formats descriptions]] | ||
+ | *[[MIPAV configuration files]] | ||
+ | |||
+ | Next: [[FAQ: Understanding Changes in MIPAV]] | ||
− | + | [[Category: FAQ]] | |
− | [[ | + | [[Category: Help]] |
Latest revision as of 15:15, 26 April 2012
Contents
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
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
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.
To use the alphablending function you need to open two or more images. In order to do that:
- Click the image you want to make an active image.
- 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.
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).