Difference between revisions of "FAQ: Understanding Image Basics"
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=== How do I save images in a different format? === | === How do I save images in a different format? === | ||
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When you save an image after working on it in MIPAV, <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">be sure to type the correct extension</font>'''</span> at the end of the file name to save the image in the correct format. | When you save an image after working on it in MIPAV, <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">be sure to type the correct extension</font>'''</span> at the end of the file name to save the image in the correct format. | ||
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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: | 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: | ||
− | <div style="font-style: normal; font-weight: normal; margin-bottom: 14pt; margin-left: 18pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> Manufacturer or application in | + | <div style="font-style: normal; font-weight: normal; margin-bottom: 14pt; margin-left: 18pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> Manufacturer or application in Table 1 <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 14pt; margin-left: 18pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> File extension in Table 2 <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"> <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. Graphics file formats supported by MIPAV listed by | + | |+ <div class="TableTitle">Table 1. Graphics file formats supported by MIPAV listed by manufacturer </div> |
|- bgcolor="#CCCCCC" | |- bgcolor="#CCCCCC" | ||
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{| | {| | ||
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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"> [ | + | <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> |
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{| border="1" cellpadding="5" | {| border="1" cellpadding="5" | ||
− | |+ <div class="TableTitle">Table 2. Graphics file formats supported by MIPAV listed by file | + | |+ <div class="TableTitle">Table 2. Graphics file formats supported by MIPAV listed by file extension </div> |
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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"> [ | + | <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>]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>2</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>3</sup>]MIPAV does not save extra information with the AFNI file. It only does the "bare minimum."<br /></font></div> |
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=== How do I combine two images for alphablending? === | === How do I combine two images for alphablending? === | ||
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{| border="1" cellpadding="5" | {| border="1" cellpadding="5" | ||
− | |+ | + | |+ '''Figure 20. File > Load menu''' |
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[[Image:menuFileLoad.jpg]] | [[Image:menuFileLoad.jpg]] | ||
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{| border="1" cellpadding="5" | {| border="1" cellpadding="5" | ||
− | |+ | + | |+ '''Figure 21. MIPAV window displaying the Active Image and Alphablending slider''' |
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[[Image:windowMIPAV_Alphablending2.jpg]] | [[Image:windowMIPAV_Alphablending2.jpg]] | ||
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|} | |} | ||
− | <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 14pt; margin-left: 18pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 4 Adjust the alphablending slider at the bottom of the MIPAV window to reveal all of the images.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 14pt; margin-left: 18pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 5 Move the slider to select the best ratio for the datasets of interest. <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 14pt; margin-left: 18pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 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 /></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-indent: 0pt; text-transform: none; vertical-align: baseline"><u><font color="#ff1621"> | + | <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 14pt; margin-left: 18pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 4 Adjust the alphablending slider at the bottom of the MIPAV window to reveal all of the images.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 14pt; margin-left: 18pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 5 Move the slider to select the best ratio for the datasets of interest. <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 14pt; margin-left: 18pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 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 /></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-indent: 0pt; text-transform: none; vertical-align: baseline"><u><font color="#ff1621"> |
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[[FAQ: Understanding Changes in MIPAV]] | [[FAQ: Understanding Changes in MIPAV]] |
Revision as of 16:53, 9 March 2012
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.
</font></span>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.
</font></div>
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
|
File Extension
|
Open
|
Save
|
---|---|---|---|
Adobe Photoshop
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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
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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
|
[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.
|
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
|
[ 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."
|
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.