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| − | =Allocating memory in MIPAV=
| + | When you run MIPAV for the first time you must specify the amount of memory that you would like to allocate, so that MIPAV can take the full advantage of the memory resources available in your machine. For more information about user permissions, memory limits, and memory usage in different operation systems, refer to: [[FAQ: Understanding Memory]]. |
| | | | |
| − | When you run MIPAV for the first time you must specify the amount of memory that you would like to allocate, so that MIPAV can take the full advantage of the memory resources available in your machine.
| + | '''Note:''' [[FAQ: Understanding Memory | MIPAV’s memory allocation]] is a program-level feature and it affects all users of a given MIPAV installation. You can only change the amount of allocated memory, if you are running MIPAV using an administrative account. |
| | | | |
| − | <div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1 Select Help > Memory allocation in the MIPAV window. The Change JavaRuntime Memory Allocation dialog box opens. See Figure 3.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000">
| + | == To allocate memory when installing MIPAV == |
| − | 2 Change the maximum heap size number so that it reflects the maximum amount of memory that should be allocated. <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 5pt; margin-left: 0pt; margin-right: 0pt; margin-top: 5pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> In a Microsoft Windows system, you can specify a maximum to 1.2 or 1.3 Gb. If additional memory is needed, MIPAV allocates it until the memory reaches the maximum heap size that you specify.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000">
| + | |
| − | 3 Click OK to close the dialog box.<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">
| + | |
| | | | |
| − | '''Figure 3. Change Java-Runtime Memory Allocation dialog box '''
| + | Refer to [[FAQ: Understanding Memory]]. |
| − | {|-
| + | |
| − | [[Image:ChangeMemoryAllocation.jpg|center]] | + | |
| − | |}<br clear="all" /><br />
| + | |
| | | | |
| | + | == To monitor memory usage == |
| | + | [[File:MemoryUsage.jpg|400px|thumb|right|The Memory Monitor dialog box]] |
| | | | |
| − | You must restart of MIPAV for the changes to take effect. To exit MIPAV, select File > Exit. Then, restart the software.
| + | When MIPAV performs a function, such as visualizing an image file, it uses memory. When the function completes (i.e., the visualized image closed), you can manually free the memory so it can be used for another function. The first step is to view how much memory is currently being used and to free needlessly reserved memory. Then, if necessary, you may need to allocate additional memory. |
| | | | |
| − | ==== To allocate additional memory ====
| + | === To determine how much memory is currently being used by MIPAV === |
| | | | |
| − | The first step is to view how much memory is currently being used and to free needlessly reserved memory. Then, if necessary, you may need to allocate additional memory. | + | <ol> |
| | + | <li>Select Help » Memory Usage in the MIPAV window. The Memory Monitor dialog box appears. </li> |
| | + | <li>The Memory Monitor dialog box shows how much memory is allocated and how much memory has been used. The vertical bar on the right of the window displays a pictorial representation of the ratio of allocated memory or amount of memory used. The chart shows the memory usage for the past 3 minutes and 45 seconds. The chart is updated every second.</li> |
| | + | <li>If you want to constantly monitor your memory resources, you can leave the Memory Monitor dialog box open on your desktop. Otherwise, close it. </li> |
| | + | </ol> |
| | | | |
| − | <div style="font-style: normal; margin-bottom: 6pt; margin-left: 0pt; margin-right: 0pt; margin-top: 14pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">To determine how much memory is currently being used by MIPAV</font>'''</span><br /></font>'''</div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1 Select Help > Memory Usage in the MIPAV window. The Memory Monitor dialog box appears (Figure 4). <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> When MIPAV performs a function, such as visualizing an image file, it uses memory. When the function completes (i.e., the visualized image closed), you can manually free the memory so it can be used for another function.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> The Memory Monitor dialog box shows how much memory is allocated and how much memory has been used. The vertical bar on the right of the window displays a pictorial representation of the ratio of allocated memory or amount of memory used. The chart shows the memory usage for the past 3 minutes and 45 seconds. The chart is updated every second.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> If you want to constantly monitor your memory resources, you can leave the Memory Monitor dialog box open on your desktop. Otherwise, close it. <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 2 Click Free memory to free memory.<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">
| + | To figure out how much memory you actually need, refer to [[FAQ: Understanding Memory#MemoryNeeded | How much memory does MIPAV require to run?]] |
| − | ''' Figure 4. Memory Monitor dialog box'''<br />
| + | |
| | | | |
| − | <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 clear="all" />
| + | == To manually free memory == |
| | | | |
| − | [[Image:MemoryMonitorDialogBox.jpg|center]] | + | [[File:GarbageCollector.jpg|frameless]] As Java-based programs run, they often leave old variables, objects, or constructors in memory. For instance, if you delineate a VOI, the coordinates of the contours may remain in memory even after you close the image. Java provides a method called the ''garbage collector'' (or ''memory recycling'') that automatically freeing objects that are no longer referenced by the program and clears all unnecessarily reserved memory. Generally, the software does this automatically when free memory becomes very limited. However, you can run the garbage collector at any time to free memory by clicking the Garbage Collector button on the main MIPAV window. You can also free memory in the Memory Monitor dialog box by clicking the Free Memory button.<br /> |
| | | | |
| | | | |
| − | <br />
| + | == To allocate additional memory == |
| | + | [[File:MemoryAllocation.jpg|429px|thumb|right| The Change java-runtime Memory Allocation dialog box]] |
| | | | |
| − | If you need more memory, you can allocate virtual memory or disk swap space if there is free space on your hard drive. For instructions on how to do this, refer to the documentation for your system. If you cannot assign more virtual memory or disk swap space, you may need to install additional memory.
| + | === For Windows users: === |
| | | | |
| − | <div style="font-style: normal; margin-bottom: 6pt; margin-left: 0pt; margin-right: 0pt; margin-top: 14pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> To manually free the memory<br /></font>'''</div> | + | <ol> |
| | + | <li> Select Help » Memory allocation in the MIPAV window. The Change JavaRuntime Memory Allocation dialog box opens.</li> |
| | + | <li>Change the maximum heap size number so that it reflects the maximum amount of memory that should be allocated. In a Microsoft Windows 32 system, you can specify a maximum of 1.3 Gb. </li> |
| | + | <li>Click OK to close the dialog box.</li> |
| | + | <li>Restart MIPAV for the changes to take effect. To exit MIPAV, select File » Exit. Then, restart the software.</li> |
| | + | </ol> |
| | | | |
| − | As Java-based programs run, they often leave old variables, objects, or constructors in memory. For instance, if you delineate a VOI, the coordinates of the contours may remain in memory even after you close the image. Java provides a method called the <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">garbage collector</font>''</span> (or <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">memory recycling</font>''</span>) that automatically freeing objects that are no longer referenced by the program and clears all unnecessarily reserved memory. Generally, the software does this automatically when free memory becomes very limited. However, you can run the garbage collector at any time to free memory by clicking the Memory Usage button. Refer to Figure 5.
| + | Now, when additional memory is needed, MIPAV allocates it until the memory reaches the maximum heap size that you specify. |
| | | | |
| − | <div style="font-style: normal; margin-bottom: 6pt; margin-left: 0pt; margin-right: 0pt; margin-top: 14pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> To allocate additional memory, <br /></font>'''</div>
| + | === For Linux users: === |
| | + | Refer to [[FAQ: Understanding Memory]]. |
| | | | |
| − | Repeat the steps described in "Allocating memory in MIPAV".
| + | === For Mac OS users: === |
| | + | Refer to [[FAQ: Understanding Memory]]. |
| | | | |
| − | <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">
| |
| − | '''Figure 5. Running the garbage collector to free the memory in MIPAV'''
| |
| − | [[Image:MemoryUsageBut.jpg]]
| |
| | | | |
| | + | === If you need even more memory === |
| | | | |
| − | <br />
| + | You can allocate virtual memory or disk swap space if there is free space on your hard drive. For instructions on how to do this, refer to the documentation for your system. If you cannot assign more virtual memory or disk swap space, you may need to install additional memory. |
| | | | |
| − | == Opening and loading image files == | + | === Memory limitations === |
| | | | |
| − | <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"> MIPAV displays images in windows, or frames, that you can move or arrange around the desktop (Figure 6). You can display as many image datasets as needed as long as your computer has enough allocated memory.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 5pt; margin-left: 0pt; margin-right: 0pt; margin-top: 5pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Note:</font>'''</span> The amount of memory required depends on the number of image datasets that are open and the size of each image file. For more information, refer to "Managing memory resources".<br />
| + | Refer to [[FAQ: Understanding Memory]]. |
| | | | |
| − | You can either open or load an image file. When you <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">open</font>''</span> an image file, MIPAV displays the image in a new image window. <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">Loading</font>''</span> an image file imports the file into an image window in which another image file is open. In other words, two image files share a common image window.
| |
| | | | |
| − | ==== Understanding image windows ==== | + | === For more information === |
| | + | Refer to: [[FAQ: Understanding Memory]]. |
| | | | |
| − | An <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">image window</font>''</span> Figure 6 consists of a title bar and an image itself.
| + | == See also: == |
| | + | *[[Opening and loading image files]] |
| | + | *[[MIPAV toolbars]] |
| | + | *[[Displaying MIPAV Toolbars]] |
| | + | *[[Displaying images]] |
| | | | |
| − | '''Figure 6. An image window'''<br />
| + | [[Category:Help]] |
| − | | + | [[Category: Getting started]] |
| − | [[Image:QuickStart_ImageWindow.jpg|center]] | + | |
| − | | + | |
| − | The title bar displays:
| + | |
| − | *the image file name, e.g. "3DHead";<br />
| + | |
| − | *the number of the current slice and the total number of slices in the dataset, e.g. 62/124;<br />
| + | |
| − | *the magnification level, e.g. M:1.0.<br />
| + | |
| − | *The number of the current slice is also shown in the lower left corner of the image.<br />
| + | |
| − | | + | |
| − | You can move an image window around your desktop by clicking the title bar and dragging the window to a new location.<br />
| + | |
| − | | + | |
| − | Sometimes, depending on the view, a toolbar or menu bar also appears in the image window. For example, the image window using the<span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000"> light box view</font>''</span> contains a toolbar and menu bar. See also [["Displaying images using the lightbox view"]].
| + | |
| − | | + | |
| − | ==== Image A and Image B ====
| + | |
| − | | + | |
| − | <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"> In MIPAV, the first image opened in an image window (see "Understanding image windows")") is referred to as <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">Image A</font>''</span>. When you load, or import, a second image in the same window, MIPAV refers to the second image as <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">Image B</font>''</span>. <br /></font></div>
| + | |
| − | | + | |
| − | === Supported formats ===
| + | |
| − | | + | |
| − | You can use MIPAV to open or load files of a variety of medical and generic graphics and multimedia file formats. Table 1 lists the format, extension, and whether MIPAV can read or write files of a particular format. The <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">extension</font>''</span>, which is the last few characters of a file name including the period, indicates the file format. For example, in the file name <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">DOE255.ima</font>''</span>, the extension <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">.ima</font>''</span> indicates that the file is stored in DICOM format. In the table, the Read column indicates that MIPAV can display image files of a particular format. When a file is read, it is stored in main memory so that MIPAV can access it. The Write column means that MIPAV can copy the data from the memory to a storage destination, such as your hard disk. In this context, <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">write</font>''</span> is synonymous with <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">save</font>''</span>.
| + | |
| − | | + | |
| − | <div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 5pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> For more information on file formats, the list of supported formats and other information, refer to Chapter 4 in the ''MIPAV User's Guide''.
| + | |
| − | | + | |
| − | ====testing====
| + | |
| − | {| border="1" cellpadding="5"
| + | |
| − | |+ <div class="TableTitle">'''Table 1. File formats that MIPAV can read and write'''</div>
| + | |
| − | |- bgcolor="#CCCCCC"
| + | |
| − | !
| + | |
| − | Manufacturer or Application
| + | |
| − | !
| + | |
| − | Extensions
| + | |
| − | !
| + | |
| − | Read
| + | |
| − | !
| + | |
| − | Write
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | AFNI
| + | |
| − | |
| + | |
| − | PSD
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | AFNI
| + | |
| − | |
| + | |
| − | HEAD, BRIK
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | Analyze
| + | |
| − | |
| + | |
| − | IMG
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | Audio Video Interleave
| + | |
| − | |
| + | |
| − | AVI
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | BIORAD
| + | |
| − | |
| + | |
| − | PIC
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |
| + | |
| − | N
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | Bruker
| + | |
| − | |
| + | |
| − | 2dseq
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |
| + | |
| − | N
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | Cheshire
| + | |
| − | |
| + | |
| − | IMG or IMC
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | DICOM
| + | |
| − | |
| + | |
| − | DCM, IMA
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | FITS
| + | |
| − | |
| + | |
| − | FTS
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |
| + | |
| − | N
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | FreeSurfer image
| + | |
| − | |
| + | |
| − | COR
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |
| + | |
| − | N
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | FreeSurfer surface (ASCII file)
| + | |
| − | |
| + | |
| − | ASC
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |
| + | |
| − | N
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | GE - Genesis 5X and LX
| + | |
| − | |
| + | |
| − | SIG
| + | |
| − | |Y
| + | |
| − | |
| + | |
| − | N
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | Graphics Interchange File
| + | |
| − | |
| + | |
| − | GIF
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |
| + | |
| − | N
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | ICS (Image Cytometry Standard)
| + | |
| − | |
| + | |
| − | ICS
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |
| + | |
| − | N
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | Interfile
| + | |
| − | |
| + | |
| − | HDR
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |
| + | |
| − | N
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | Joint Photographics Experts Group
| + | |
| − | |
| + | |
| − | JPEG, JPG
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | Laser Scanning Microscope
| + | |
| − | |
| + | |
| − | LSM
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | Macintosh PICT
| + | |
| − | |
| + | |
| − | PICT
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | Medical Image Network <br />
| + | |
| − | Common Data Form including ROIs
| + | |
| − | |
| + | |
| − | MNC
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |-
| + | |
| − | |MICRO-CAT
| + | |
| − | |
| + | |
| − | LOG
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |
| + | |
| − | N
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | Microsoft Windows Bitmap
| + | |
| − | |
| + | |
| − | BMP, DIB
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | Medical Research Council
| + | |
| − | |
| + | |
| − | MRC
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | NIFTI
| + | |
| − | |
| + | |
| − | Dual file (.HDR & .IMG) or single file (.NII) storage
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | PC Paintbrush
| + | |
| − | |
| + | |
| − | PCX, DCX, PCC
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | Portable Network Graphic
| + | |
| − | |
| + | |
| − | PNG
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |-
| + | |
| − | QuickTime-Apple
| + | |
| − | |
| + | |
| − | QT, MOV
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | RAW
| + | |
| − | |
| + | |
| − | RAW
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | Siemens - Magnetom Vision
| + | |
| − | |
| + | |
| − | IMA
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |
| + | |
| − | N
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | Sun Raster
| + | |
| − | |
| + | |
| − | RS, RAS
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | Tag Image File Format
| + | |
| − | |
| + | |
| − | TIFF
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | Truevision Graphics Adapter
| + | |
| − | |
| + | |
| − | TGA, VST, VDA, ICB, TPIC
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | X BitMap
| + | |
| − | |
| + | |
| − | XBM
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | XML
| + | |
| − | |
| + | |
| − | XML
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | X PixMap
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | |
| + | |
| − | Y
| + | |
| − | }</tr>
| + | |
| − | </table></div><br />
| + | |
| − | }
| + | |
| − | | + | |
| − | ==== Image Browser ====
| + | |
| − | <div style="font-style: normal; margin-bottom: 3pt; 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"> Figure 7. Choose Image Filter dialog box<br /></font>'''</div>
| + | |
| − | | + | |
| − | {| border="1" cellpadding="5"
| + | |
| − | |+
| + | |
| − | |-
| + | |
| − | | rowspan="1" colspan="2" |
| + | |
| − | You can select the image formats to display using the File > Open Image(A) > Image Browser menu. This opens the <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Choose Image Filter dialog box</font>'''</span>. In this dialog box, use the check boxes to select the image types which you would like to use in MIPAV.
| + | |
| − | | rowspan="2" colspan="1" |
| + | |
| − | <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 clear="all" />
| + | |
| − | [[Image:ChooseImageFilter.jpg|center]]
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | Select All
| + | |
| − | |
| + | |
| − | Selects all image types.
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | Clear
| + | |
| − | | rowspan="1" colspan="2" |
| + | |
| − | Removes selection.
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">OK</font>'''</span>
| + | |
| − | | rowspan="1" colspan="2" |
| + | |
| − | Applies the image type selection to MIPAV.
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Cancel</font>'''</span>
| + | |
| − | | rowspan="1" colspan="2" |
| + | |
| − | Disregards any changes you made in this dialog box and closes the dialog box.
| + | |
| − | |}
| + | |
| − | | + | |
| − | </font></span><br /></font></div>
| + | |
| − | | + | |
| − | === Opening image files ===
| + | |
| − | | + | |
| − | <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"> The <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Open Image A from disk</font>'''</span> menu allows you to open an image which is stored on your hard drive (or network drive).<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"
| + | |
| − | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure 8. File > Open menu <br /></font>'''</div>
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | <div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 1pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <br clear="all" />
| + | |
| − | |[[Image:MIPAV_QS_OpenFile.jpg|center]]
| + | |
| − | |}<br clear="all" /><br /></font></div>
| + | |
| − | |}
| + | |
| − | | + | |
| − | <br /></font></div><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"> The <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Open Image A </font>'''</span>menu (Figure 8]) provides you with additional options such as to open a single image file, or image sequence, or Leica series images - the images that were taken on a Leica microscope. You can also call Create Blank Image to create a blank image (refer to "Creating new images").<br /></font></div><div style="font-style: normal; margin-bottom: 6pt; margin-left: 0pt; margin-right: 0pt; margin-top: 14pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> To open an image file or multifiles <br /></font>'''</div>
| + | |
| − | | + | |
| − | An option on the Open Image dialog box (Figure 8), which appears after you select File > Open Image(A), is <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Open as multifile</font>'''</span>. This option lets you open the image as a <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">multifile</font>''</span>.
| + | |
| − | | + | |
| − | <div style="font-style: normal; font-weight: normal; margin-bottom: 5pt; margin-left: 0pt; margin-right: 0pt; margin-top: 5pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">Multifiles</font>''</span> are image datasets that are composed of multiple files.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000">
| + | |
| − | 1 Select File > Open Image(A) from disk. The Open Image dialog box (Figure 9) opens.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000">
| + | |
| − | 2 Navigate to the directory where the file is stored. <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000">
| + | |
| − | 3 Select an image file.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000">
| + | |
| − | 4 To open the image file as a multifile, select the <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Open as multifile</font>'''</span> box.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> The name of the image appears in File Name.<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"
| + | |
| − | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure 9. Open as Multifile option<br /></font>'''</div>
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | <div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 1pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <br clear="all" />
| + | |
| − | |
| + | |
| − | [[Image:OpenAsMultifile.jpg|center]]
| + | |
| − | |}<br clear="all" /><br /></font></div>
| + | |
| − | | + | |
| − | | + | |
| − | <br /></font></div><div style="font-style: normal; margin-bottom: 6pt; margin-left: 0pt; margin-right: 0pt; margin-top: 14pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> If you can't find the image, <br /></font>'''</div>
| + | |
| − | | + | |
| − | check the files types listed in Files of Type (showing in Figure 9) near the bottom of the dialog box. If the file type you are looking for does not appear in Files of Type, select All Files or All.
| + | |
| − | | + | |
| − | <div style="font-style: normal; margin-bottom: 6pt; margin-left: 0pt; margin-right: 0pt; margin-top: 14pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> To form a 4D dataset in Analyze format, <br /></font>'''</div>
| + | |
| − | | + | |
| − | use <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Open as multifile</font>'''</span> to open a series of individual 3D Analyze, formatted, consecutively ordered images.For example, you can use Open as multifile to open an array of TIFF, JPEG, BMP, etc., files if their file names meet the following format: <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">f</font>''</span><span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">oo</font>''</span>_001.<span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">tiff</font>''</span>, <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">foo</font>''</span>_002.<span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">tiff</font>''</span>, <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">foo</font>''</span>_003, etc. where <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">foo</font>''</span> is the name of the file.
| + | |
| − | | + | |
| − | <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>
| + | |
| − | | + | |
| − | === MIPAV window ===
| + | |
| − | | + | |
| − | After the first image is opened, the MIPAV window changes. It includes more menus, the title bar displays more information, and tool bars appear. Because the MIPAV window is context sensitive, it displays or hides commands on the menus depending on the characteristics of the image file that is opened. If you opened a dataset file that contains more than one image, an <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">image slice slider</font>''</span> also appears. Refer to Figure 10.
| + | |
| − | | + | |
| − | | + | |
| − | {| border="1" cellpadding="5"
| + | |
| − | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure 10. Expanded MIPAV window showing toolbars, image slider, and more menus after the first image is opened. See also "MIPAV toolbars".
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | <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 clear="all" />
| + | |
| − | |
| + | |
| − | [[Image:ExpandedMIPAVWindow.jpg|center]]
| + | |
| − | |}<br clear="all" /><br /></font></div>
| + | |
| − | | + | |
| − | | + | |
| − | <br /></font></div>
| + | |
| − | | + | |
| − | If you prefer for MIPAV to use the style of Open and Save dialog boxes that are used by the operating system (e.g., Microsoft Windows, Unix, or Apple) on your computer, read the section on "Using platform-specific Open and Save dialog boxes".
| + | |
| − | | + | |
| − | === Loading image files ===
| + | |
| − | | + | |
| − | <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"> When you <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">load</font>''</span> an image file, MIPAV imports it into an existing image window. The loaded image shares the same window with another image file. Loading a file allows you to compare two datasets. <br /></font></div><div style="font-style: normal; margin-bottom: 6pt; margin-left: 0pt; margin-right: 0pt; margin-top: 14pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> To load an image file<br /></font>'''</div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1 Open the first image by selecting File > Open Image(A) from disk. The image appears in an image window. <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 2 Select the title bar of the image window (in this case, the image that you just opened) in which you want to load another image. <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 3 Select one of the following: <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 36pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">File > Load Image (B) > From Frame</font>'''</span> to load another image dataset from an already opened image dataset;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 36pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">File > Load Image (B) > From File</font>'''</span> to load another image dataset;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 36pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">File > Load Image (B) > Create a Blank Image </font>'''</span>to create a blank image.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 4 If you chose Image (B) from File, the Open dialog box appears, see [MIPAV_QuickStart.html#2614455 Figure 9]. Select the image file you want to load, and click OK.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> If MIPAV does not recognize the type of file based on its extension, the Choose Image Filter dialog box opens (see also [MIPAV_QuickStart.html#2697974 "Image Browser" on page 16]). Here, select the file type and click OK.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> As the image file is loading, a pop-up window appears with the status. When the image file finishes loading, it appears in the image window. At this point, take note of several changes:<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 36pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> MIPAV pseudo-color was applied to the images in the image frame. The pseudo-color indicates that two images are loaded in the same image frame.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 36pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> In the MIPAV window, the Active Image and Alphablending slider appears. The slider allows you to control which image is displayed in the foreground of the window. The image in the foreground is the <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">active image</font>''</span>. You can adjust the translucency of the alpha channels in each image using the technique.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 5 If you chose Image (B) from Frame, the Load Image onto <file name> ([MIPAV_QuickStart.html#2754711 Figure 11]) opens. Select one of the images in Set as Image (B), and then click OK. The image is loaded onto the first image file.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 5pt; margin-left: 0pt; margin-right: 0pt; margin-top: 5pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Note:</font>'''</span> The abbreviations <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">(A)</font>''</span> or <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">(B)</font>''</span> appear after some commands. <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">(A)</font>''</span>, which is the abbreviation for "Image A," indicates that the option is applied to the first image opened in an image window. <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">(B)</font>''</span>, 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.<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">
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| − | <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 5pt; margin-left: 0pt; margin-right: 0pt; margin-top: 5pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Note:</font>'''</span> MIPAV recognizes files types by the file extension. For example, if you select an image named "Smith.tiff", MIPAV tries to open the file as a TIFF file. If that image is actually a <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">JPEG</font>''</span> file and mistakenly has the <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">TIFF</font>''</span> extension, MIPAV fails to open the file.<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"> <br /></font></div>
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When you run MIPAV for the first time you must specify the amount of memory that you would like to allocate, so that MIPAV can take the full advantage of the memory resources available in your machine. For more information about user permissions, memory limits, and memory usage in different operation systems, refer to: FAQ: Understanding Memory.
When MIPAV performs a function, such as visualizing an image file, it uses memory. When the function completes (i.e., the visualized image closed), you can manually free the memory so it can be used for another function. The first step is to view how much memory is currently being used and to free needlessly reserved memory. Then, if necessary, you may need to allocate additional memory.
Now, when additional memory is needed, MIPAV allocates it until the memory reaches the maximum heap size that you specify.
You can allocate virtual memory or disk swap space if there is free space on your hard drive. For instructions on how to do this, refer to the documentation for your system. If you cannot assign more virtual memory or disk swap space, you may need to install additional memory.
As Java-based programs run, they often leave old variables, objects, or constructors in memory. For instance, if you delineate a VOI, the coordinates of the contours may remain in memory even after you close the image. Java provides a method called the garbage collector (or memory recycling) that automatically freeing objects that are no longer referenced by the program and clears all unnecessarily reserved memory. Generally, the software does this automatically when free memory becomes very limited. However, you can run the garbage collector at any time to free memory by clicking the Garbage Collector button on the main MIPAV window. You can also free memory in the Memory Monitor dialog box by clicking the Free Memory button.
