Difference between revisions of "Registration: Manual 2D Series"

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The Manual 2D Series algorithm allows you to manually or semimanually register two 2D grayscale or color images by placing corresponding points on both images and then applying either the Landmark-Thin Plate Spline or Landmark-Least Squares algorithm. After applying one of these algorithms, you can then, if needed, use the other algorithm. In addition, at any time, you can manually adjust the alignment of each image.<br />
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[[Image:mipavfinallogo.gif]]
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----
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The algorithm also lets you manually register different slices of a 2.5 image dataset in the same way as the 2D images.
  
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== Manual 2D Series ==
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== Background ==
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[[File:WindowManual2D.jpg|400px|thumb|right|Registration: Manual 2D Series window]]
  
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The Manual 2D Series algorithm allows you to manually or semi manually register two 2D grayscale or color images by placing corresponding points on both images, and then applying either the Landmark-Thin Plate Spline or Landmark-Least Squares algorithm. After applying one of these algorithms, you can then, if needed, use the other algorithm. In addition, at any time, you can manually adjust the alignment of each image.
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Through the Registration: Manual 2D Series window (Figure 1), this algorithm provides the tools for manually registering images and the ability to use two of the landmark registration algorithms. The Registration: Manual 2D Series window includes two tabs: Blended and Dual.<br />
  
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The algorithm also lets you manually register different slices of a 2.5D and 3D image datasets in the same way as 2D images. See also [Manual2DSeriesOV.html#wp1863964 "Applying the Manual 2D Series algorithm to 2.5D images" ] and [Manual2DSeriesOV.html#wp1866667 "Applying the Manual 2D Series algorithm to 3D images" ].
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<div id="BlendedTab"><div>
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=== Blended tab ===
  
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=== Background ===
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'''On the Blended page''', the window superimposes the image to be registered on top of the reference image. This page includes icons for aligning, rotating, alphablending, and magnifying or minifying the images as well as icons for modifying the lookup table for each image and for applying a checkerboard pattern to assist in alignment.
  
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Through the Registration: Manual 2D Series dialog ([Manual2DSeriesOV.html#wp1849182 Figure 6]), this algorithm provides the tools for manually registering images, as well as the ability to use two of the landmark registration algorithms-Thin Plate Spline and Least Squares.
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<div id="DualTab"><div>
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=== Dual tab ===
  
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The following tools are available for manually registering images:
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Clicking the Dual tab opens the Dual page, which displays the images side by side. A number of icons appear in the toolbar. The red icons are color coded to the reference image, which appears on the left and is surrounded by a red border. The green icons apply to the image to be registered, which is shown on the right side of the page and is surrounded by a green border.
  
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* [Manual2DSeriesOV.html#wp1856093 "Changing displaying proportion" ]
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[[File:Manual2DSeriesDualTab.jpg|300px|thumb|center|The Dual page displays the images side by side]]
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* [Manual2DSeriesOV.html#wp1860034 "Moving the adjusted image" ]
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* [Manual2DSeriesOV.html#wp1862562 "Rotating the adjusted image" ]
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* [Manual2DSeriesOV.html#wp1863828 "Delineating the landmark points" ]
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* [Manual2DSeriesOV.html#wp1858224 "Applying the image registration algorithms" ]
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==== Image types ====
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=== Delineating corresponding points ===
  
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You can apply this algorithm to 2D, 2.5 D, and 3D grayscale and color images. The dimensions or image type of the adjusted image need not be the same as the dimensions or image type of the reference image. The adjusted image has the same image type and the same extents as the reference image. See also: [Manual2DSeriesOV.html#wp1846362 "Applying the Manual 2D Series algorithm on 2D images"], [Manual2DSeriesOV.html#wp1863964 "Applying the Manual 2D Series algorithm to 2.5D images"], and [Manual2DSeriesOV.html#wp1866667 "Applying the Manual 2D Series algorithm to 3D images"].
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Before being able to use either the Thin Plate Spline or Least Squares algorithm, you must first delineate a minimum of three corresponding points on both images. These points serve as guides, or landmarks, for aligning the images. In order for the points to be corresponding, you should delineate each point in the same sequence; i.e., the first point that you delineate on the reference image should be the first point delineated on the image to be registered, the second point on the reference image should be the second point delineated on the image to be registered, and so on.
  
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==== Special notes ====
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To delete a point, you must first select the point and then use the appropriate Delete icon to delete it. However, before you can select the point, you need to return the cursor to its default mode using the [[Image:IconReturntoDefaultMode.jpg]] icon.
  
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For 2D, 2.5D and 3D images, three or more landmark points are required. The algorithm may fail if nearly all of the points fall on the same line.
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On both the Blended and Dual pages, you can modify the lookup table (LUT) by clicking [[Image:IconLookupTable.jpg]] , the LUT icon. When you select [[Image:IconLookupTable.jpg]] , the Lookup Table window appears. This window includes two tabbed pages: one for Image A, the reference image, and one for Image B, the image to be registered.
  
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==== References ====
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A common icon-[[Image:IconReset.jpg]] , the Reset icon-appears on both the Blended and Dual pages. Use this icon if you want to restore the original version of the images. This icon deletes all points on the reference image and on the image to be registered.
  
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"Least-Squares Fitting of Two 3-D Point Sets" by K.S. Arun, T.S. Huang, and S.D. Blostein, IEEE Transactions on Pattern Analysis and Machine Intelligence, Vol. PAMI-9, No. 5, September, 1987, pp. 698-700.
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<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> If the Apply button has already been selected, the Reset icon undoes all changes that occurred since the last time the Apply button was selected. <br /></font></div>
  
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David Eberly, "Thin Plate Splines" of Magic Software at http://www.magic-software.com. Also at the same site are the files: MgcInterp2DThinPlateSpline.h, MgcInterp2DThinPlateSpline.cpp, MgcInterp3DThinPlateSpline.h, MgcInterp3DThinPlateSpline.cpp Paper that explains warping from one ''x,y'' source to another ''x,y'' target set.
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== Image types ==
  
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Fred L. BookStein, "Principal Warps: Thin-Plate Splines and the Decompositions of Deformations," ''IEEE Transactions on Pattern Analysis and Machine Intelligence'', Vol. 11, No. 6, June 1989, pp. 567-585.
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You can apply this algorithm to 2D grayscale and color images.  
  
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=== Applying the Manual 2D Series algorithm on 2D images ===
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The dimensions or image type of the image to be registered need not be the same as the dimensions or image type of the reference image. The registered image has the same image type as the image to be registered and the same extents as the reference image.
  
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===== To run this algorithm, complete the following steps: =====
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== Special notes regarding the number of references points ==
  
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# Open two images- the reference image and the image you want to register or'' adjusted image.''
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The following notes apply:
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# Select the reference image.
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# Select Algorithms &gt; Registration &gt; Manual 2D Series. The Load dialog box appears. See [Manual2DSeriesOV.html#wp1849182 Figure 6].
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*For 2D images, three or more points are required. The algorithm may fail if nearly all of the points fall on the same line.  
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# Select the image that you want to register to the reference image. '''Note that, '''if only two images are open, the Set as Image B box automatically selects the other open image-the one you did not select-as Image B or ''adjusted image''. See [Manual2DSeriesOV.html#wp1849182 Figure 6].
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*For 3D images, four or more points are required and the algorithm may fail if the points nearly all fall on the same plane.
  
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<div>.<div align="left">[[Image:dialogboxLoad48.jpg]]</div> </div>
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div id="ApplyingOn2D"><div>
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<div id="ApplyingOnTwoD"><div>
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== Applying the Manual 2D Series algorithm on 2D images ==
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[[File:DialogBoxLoada.jpg|200px|thumb|right|The Load dialog box]]
  
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# To select a different image, select the File option, and then click Browse to find and open another image.
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1 Open two images: the reference image and the image that you want to register.
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# Click OK.
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2 Select the reference image.
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# The Manual 2D Series window opens. By default, the window opens in Blended mode. Note that, opening this window automatically corrects image resolution and scaling.
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3 Select Algorithms > Registration > Manual 2D Series. The Load dialog box appears.
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4 Select the image that you want to register to the reference image. If only two images are open, the Set as Image B box automatically selects the other open image-the one you did not select-as Image B, or the image to be registered.
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5 To select a different image, click Browse to find and open another image file.
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6 Click OK. The Manual 2D Series window opens.
  
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As shown in [Manual2DSeriesOV.html#wp1847549 Figure 7], the Registration: Manual 2D Series window has the main menu (see below) and two tabs: Blended and Dual. Refer to [Manual2DSeriesOV.html#wp1847428 "Blended tab" ] and [Manual2DSeriesOV.html#wp1857731 "Dual tab" ].
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'''Note:''' Opening this window automatically corrects image resolution and scaling. The algorithm window includes two tabs:
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Blended, which displays the Blended page
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Dual, which displays the Dual page
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The Blended page shows both images: the image to be registered superimposed on top of the reference image. Note that the icons near the top of the page allow you to move the image to be registered in all directions or specifically up, down, left, and right a certain number of pixels. You can also rotate the image to be registered clockwise or counterclockwise.
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7 Click Dual to go to the Dual page.
  
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===== {| border="1" cellpadding="5" |+  |- | <div>File </div> | <div>''Close Registration''  </div> | <div>Closes this dialog without saving the images. </div> |- |  | <div>Show VOIs in blended window </div> | <div>On the Blended tab, displays the VOIs that you've delineated on the Dual tab. </div> |- |  | <div>Thin plate spline for intensity </div> | <div>Uses the Thin Plate Spline algorithm for calculating intensity values. See also [RegistrationLandmarkTPSpline.html#wp1275364 "Registration: Landmark-TPSpline"]. </div> |- | <div>Help </div> |  | <div>Runs help for this dialog box. </div> |}  Options available via the dialog menu =====
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The Dual page shows both the reference image and the image to be registered side by side in the image area at the bottom of the page.
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Note that the border around the reference image, the image on the left side of the page, appears in red. The border around the image to be registered, which is on the right side of the page, appears in green. Several of the icons near the top of the page are color coded to the images. That is, the red icons apply to the reference image, and the green icons apply to the image to be registered.
  
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=== Blended tab ===
 
  
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The Blended tab shows both images: the adjusted image superimposed on top of the reference image. By default, the image frame shows both images blended in proportion 50/50.
 
  
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==== Changing displaying proportion ====
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8 Place at a minimum three landmarks, or points, on each of the images.  On the reference image, click [[Image:IconReferenceSliceMarkers.jpg]] , the Reference Slice Markers icon, and click the mouse on the reference image where the landmark should be located. The landmark appears on the image in red type and is sequentially numbered. Create at least two more landmarks on the image.
  
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You can use the AlphaBlending image slider to change the displaying proportion towards either increasing the amount of the reference image (the Ref.R side of the slider) or adjusted image (the Adj.A side of the slider) displayed. The image slider is located at the top of the Blended tab. See also [Manual2DSeriesOV.html#wp1847549 Figure 7] and Section: [Manual2DSeriesOV.html#wp1856133 "Moving and rotating the adjusted image" ].
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On the image to be registered, click [[Image:IconAdjustedSliceMarkers.jpg]] , the Adjusted Slice Markers icon, and creates a landmark on the image by clicking the mouse. The landmark, which is sequentially numbered, appears in green type. Create a minimum of three landmarks on the image.
  
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<div>
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To delete a point on the reference image, you need to return the cursor to its default mode by clicking on [[Image:IconReturntoDefaultMode.jpg]] . You can then select the point by clicking on it with the mouse and then delete it by clicking [[Image:IconDeleteSelectedReferenceSliceMarkers.jpg]] , the Delete selected reference slice markers icon.
  
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{| border="1" cellpadding="5"
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To delete a point on the image to be registered, or adjusted image, click [[Image:IconReturntoDefaultMode.jpg]] , select the point, and then delete it by clicking [[Image:IconDeleteSelectedAdjustedSliceMarkers.jpg]] , the Delete adjusted slice markers icon.
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|+ <div>'''Figure 7. The Blended tab and the image slider''' </div>
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9 Select, if desired, either [[Image:IconLeastSquaresAlignment.jpg]] , the Least Squares algorithm icon, or [[Image:IconThinPlateSplineAlignment.jpg]] , the Thin Plate Spline algorithm, to register the images. The program registers the images and the landmarks appear in yellow type followed by the specific positions in parentheses.
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<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 size="2pt"><font color="#000000"><div><center>[[Image:ImageSlider.jpg]]</center></div><br /> </font></font></div>
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|}
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10 At this point, you should determine the following: Whether there is a need to make manual adjustments to the registration. If so, return to the Blended page and use the direction or the rotation icons. Use [[Image:IconWindowRegionofImageB.jpg]] to verify alignment (refer to [RegistrationManual2DSeries.html] and to the following tables for more information.
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Whether to run the other algorithm. If so, simply click either [[Image:IconLeastSquaresAlignment.jpg]] , the Least Squares algorithm, or [[Image:IconThinPlateSplineAlignment.jpg]] Thin Plate Spline algorithm, as appropriate.
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Whether to restore the image to its original form by clicking [[Image:IconResetImagetoOriginalState.jpg]].
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Whether to select Apply to keep changes made by the algorithm.
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== Making manual adjustments to the image to be registered ==
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<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"> After you apply either [[Image:IconLeastSquaresAlignment.jpg]] , the Least Squares algorithm icon, or <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">[[Image:IconThinPlateSplineAlignment.jpg]] </font>'''</span>, the Thin Plate Spline algorithm on the images, you may want to manually ascertain whether key portions of the reference image and the image to be registered, or adjusted image, are in alignment. One way of checking alignment, or registration, is using <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">[[Image:IconWindowRegionofImageB.jpg]] , the Window region of image B icon. </font></span>A recommended method for checking registration and for correcting it follows.<br /></font></div>
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== Checking registration ==
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=== To check registration, do the following:===
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1 Click Blended in the Manual 2D Series window to display the Blended page. Both the reference image and the image to be registered, or adjusted image, appear at the bottom of the window. The adjusted image is superimposed over the reference image.
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2 Note that the arrow on the Alphablending slider appears in the middle of the slider at 0.5R/A, which means that 50 percent of each image are shown on the page.
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3 Slide the arrow on the Alphablending slider all the way to the right until it reaches the label "Adj. A." This label indicates that 100 percent of the adjusted image is displayed on the page and, therefore, the reference image does not appear.
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Note: The label "0.75A" means that 75 percent of the adjusted image appears and only 25 percent of the reference image is displayed.
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4 Click IconLookupTable.jpg , the Lookup Table icon, to display the Lookup Table window. Note that the window includes two tabs: one for Image A, the reference image, and one for Image B, the image to be registered.
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5 Drag the image intensity line for the red channel up in the middle to adjust the color of the adjusted image. In this case, it creates a lighter colored red. The adjusted image now appears in pale red.
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Note: Actually, you can change the color of the image to any color. The purpose in doing this task is to easily distinguish the adjusted image from the reference image.
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6 Move the slider arrow all the way to the left on the slider. The label "Ref. R" indicates that the page now displays 100 percent of the reference and does not display the adjusted image.
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7 Click IconWindowRegionofImageB.jpg and position the cursor over the reference image. Notice that a square box appears on the image. The box is filled with a red image, which is the adjusted image. You can use this box to look at the alignment of details in the images.
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'''Tip:''' You may want to maximize the window and enlarge the images so that you can view details of the images while checking alignment. To maximize the window, simply click File:ButtonRestore.jpg , the Restore button. To maximize the image, click the Magnify image 2.0x icon, which magnifies the image to twice its current size, as many times as needed.
  
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</div>
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8 Determine whether you want to correct the alignment of the images. If you do, there are several ways to move the adjusted image:
  
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==== The Blended tab options: ====
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*Moving the image using [[Image:IconTranslateImage.jpg]],the Translate image icon;
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*Moving the image using the direction arrows;
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*Setting the number of pixels to move the image with the Set pixel increment icon;
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*Rotating the image.
  
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<div>
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==== Moving the adjusted image in any direction ====
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<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 Translate image icon, or <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">[[Image:IconTranslateImage.jpg]] </font></span>, allows you to move the adjusted image in any direction. This icon only appears on the Blended page, which is where all manual adjustments to image registration occurs. <br /></font></div>
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<span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">To move the adjusted image, click [[Image:IconTranslateImage.jpg]] , and, holding down the left mouse button, drag the icon in the direction in which to move the image, and then release the mouse button. After a few moments, the image appears in the new position. Note that, depending on where you moved the adjusted image, its outer portions may disappear beyond the outer edges of the reference image </font></span><span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">(see Figure 3).<span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">). In this case, you can use [[Image:IconTranslateImage.jpg]] to move the adjusted image again.</font></span>
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<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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<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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==== Moving the adjusted image with the direction arrows ====
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The icons that display direction arrows (<span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">[[Image:IconMoveImageUp.jpg]] </font></span>, the Move image up icon; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">[[Image:IconMoveImageDown.jpg]] </font></span>, the Move image down icon; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">[[Image:IconMoveImageRight.jpg]] </font></span>, the Move image right icon; and <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">[[Image:IconMoveImageLeft.jpg]] </font></span>, the Move image left icon) let you move the adjusted image in one direction only by a specified number of pixels. The default number of pixels is 1; however, the number of pixels may be from 0.01 to 2048.0. Therefore, the direction arrows provide the greatest specificity in moving the image, which is perfect for fine adjustments.
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To change the number of pixels, click <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">[[Image:IconSetPixelIncrement.jpg]] </font></span>, the Set pixel increment icon; enter a number in the Pixel Increment box; and click Apply.
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==== Rotating the adjusted image ====
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<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"> If the rotation of the adjusted image is incorrect, you can change the rotation of the image with the rotation icons: <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">[[Image:IconRotateImage.jpg]] </font></span>, the Rotate image icon; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">[[Image:IconRotateClockwise.jpg]] </font></span>, the Rotate clockwise icon; and [[Image:IconRotateCounterClockwise.jpg]] , the Rotate counterclockwise icon.<br /></font></div>
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To select the center of rotation for the image, click [[Image:IconRotateImage.jpg]] and set the center by clicking with the mouse on the image. The letter <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">C</font>''</span> appears with a yellow crosshair cursor (see Figure 4]). You can then drag a line from the center of rotation to move the image above or below the center of rotation. To rotate the image clockwise, click <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">[[Image:IconRotateClockwise.jpg]] </font></span><nowiki>; and to rotate the image counterclockwise, click </nowiki>[[Image:IconRotateCounterClockwise.jpg]] .
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As with the direction arrow icons, you change the degree increment to achieve exact registration. The default degree increment is 1.0, but you can specify from 0.01 to 360 degrees. To change the degree increment, click <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">[[Image:IconSetPixelIncrement.jpg]] </font></span>, the Set degree increment icon. The Change Degree Increment dialog box appears. Enter the degree increment in the Degree Increment box, and click Apply.
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 +
=== Registration: Manual 2D Series: Blended tab ===
  
 
{| border="1" cellpadding="5"
 
{| border="1" cellpadding="5"
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|+ <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"> Manual 2D Series window showing the Blended page <br /></font>'''</div>
 
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<div>'''[[Image:LUTIco.jpg]] Display Lookup table''' </div>
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<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Show VOIs in blended window</font>'''</span></div>
 
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<div>Opens the Lookup table dialog box. For the Lookup table (LUT) dialog box options, refer to MIPAV User's Guide, Volume 1, Basics, [MIPAV_VisualizationTools.html#wp1171332 Figure 120] "Look-up Table window". See also [Manual2DSeriesOV.html#wp1866423 "Using LUT to arrange the images" ]. </div>
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<div class="CellBody">Displays, on the Blended page, the VOIs that you delineated on the Dual page.</div>
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<div><div><center>[[Image:LooupTableDialog.jpg]]</center></div> </div><div><br /> </div><div><br /> </div><div><br /> </div><div><br /> </div><div><br /> </div><div><br /> </div><div><br /> </div><div><br /> </div><div><br /> </div><div><br /> </div><div><br /> </div><div><br /> </div>
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<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Blended tab</font>'''</span></div>
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| rowspan="1" colspan="2" |
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<div class="CellBody">Displays the Blended page, which shows the image to be registered superimposed on the reference image. This page allows you to move and align the image to be registered with the reference image.</div>
 
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<div>'''[[Image:ChessBoardIco.jpg]] Checker Board''' </div>
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<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Dual tab</font>'''</span></div>
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| rowspan="1" colspan="2" |
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<div class="CellBody">Displays the Dual page, which shows each image side by side, and allows you to delineate three or more landmarks on each image before you apply the Landmark-Least Squares algorithm or the Landmark-Thin Plate Spline algorithm to the images.</div>
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|
−
<div>The checkerboard tool displays both portions of both images in an alternating fashion, much like the squares on a checkerboard. Portions of the reference image (Image A) appear where the light-colored squares would appear on the checkerboard; portions of the adjusted image (Image B) appear in place of the dark-colored squares.  </div><div>You can use the Checkerboard pattern dialog box options to adjust the number of rows and columns displayed.  </div><div>See also MIPAV User's Guide, Volume 1, Basics, [MIPAV_VisualizationTools.html#wp1171090 Figure 116] for more infromation about the checkerboard tool. </div>
+
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Alphablending slider</font>'''</span></div>
 +
| rowspan="1" colspan="2" |
 +
<div class="CellBody">Adjusts the translucency of the alpha channels in each image using the alphablending technique. 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.</div>
 +
|-
 
|
 
|
−
<div><div><center>[[Image:CheckerBoardPIcture.jpg]]</center></div> </div><div><br /> </div><div><div><center>[[Image:CheckerBoardPatternDB.jpg]]</center></div> </div>
+
<div class="CellBody">[[Image:IconLookupTable.jpg]] <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Lookup table</font>'''</span></div>
 +
| rowspan="1" colspan="2" |
 +
<div class="CellBody">Displays the Lookup Table window, which includes two tabs: Image A, the reference image, and Image B, the image to be registered.</div>
 
|-
 
|-
 
|
 
|
−
<div>'''[[Image:ZoomIn.jpg]] Magnify image 2.0x ''' </div>
+
<div class="CellBody">[[Image:IconCheckerboard.jpg]] <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Checkerboard A &amp; B</font>'''</span></div>
 
| rowspan="1" colspan="2" |
 
| rowspan="1" colspan="2" |
−
<div>Magnifies the images 2x''n'' times. </div>
+
<div class="CellBody">Displays a checkerboard pattern on the images. You can use this pattern for assistance in aligning the images.</div>
 
|-
 
|-
 
|
 
|
−
<div>'''[[Image:ZoomOut.jpg]] Magnify image 0.5x''' </div>
+
<div class="CellBody">[[Image:RegistrationManual2DSeries39.gif]] <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Magnify image 2.0x</font>'''</span></div>
 
| rowspan="1" colspan="2" |
 
| rowspan="1" colspan="2" |
−
<div>Magnifies the images 0.5x''n'' times; or minifies the images 2x''n'' times, which is the same. </div>
+
<div class="CellBody">Doubles the size of images, magnifying them to twice their current size. If an image is too large for the current window size, scroll bars appear, and you may need to manually adjust the size of the window.</div> <div class="CellBody">To restore an image to its original size, use [[Image:IconMinifyImage.jpg]] , the Magnify image 0.5x icon, as many times as you used this icon.</div>
 
|-
 
|-
 
|
 
|
−
<div>'''[[Image:WindowRegion.jpg]] Window region of Image B''' </div>
+
<div class="CellBody">[[Image:IconMinifyImage.jpg]] <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Magnify image 0.5x</font>'''</span></div>
−
|
+
| rowspan="1" colspan="2" |
−
<div>Displays the window filled only with the adjusted image (Image B) over the reference image.'' ''You can use this window to look at the alignment of details in the images. </div>
+
<div class="CellBody">Reduces the magnification level of images in half. To restore images to their original size, use the Magnify image 2.0x icon, as many times as you used this icon.</div>
−
|
+
−
<div><div><center>[[Image:WindowRegion1.jpg]]</center></div> </div>
+
 
|-
 
|-
 
|
 
|
−
<div>'''[[Image:ResetOriginal.jpg]] Reset image to its original state''' </div>
+
<div class="CellBody">[[Image:IconWindowRegionofImageB.jpg]] <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Window region of image B</font>'''</span></div>
 
| rowspan="1" colspan="2" |
 
| rowspan="1" colspan="2" |
−
<div>Restores image to its original state. This icon also deletes all landmark points on the reference image and on the adjusted image.''' '''If the Apply button has already been selected, the Reset icon undoes all changes that occurred since the last time the Apply button was selected.  </div>
+
<div class="CellBody">Hides the reference image below a windowed mouse cursor; slide alphablending slider to the reference image</div>
 
|-
 
|-
 
|
 
|
−
<div>Apply </div>
+
<div class="CellBody">[[Image:IconResetImagetoOriginalState.jpg]] <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Reset image to original state</font>'''</span></div>
 
| rowspan="1" colspan="2" |
 
| rowspan="1" colspan="2" |
−
<div>Commits the changes that you made to the images, but it leaves the window open for you to make further changes, if desired. </div>
+
<div class="CellBody">Restores image to its original state. This icon deletes all points on the reference image and on the image to be registered.<span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000"> </font>'''</span>If the Apply button has already been selected, the Reset icon undoes all changes that occurred since the last time the Apply button was selected. </div>
 
|-
 
|-
 
|
 
|
−
<div>[[Image:TranslateIco.jpg]]Translate image </div>
+
<div class="CellBody">[[Image:btnApply.jpg]] <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Apply</font>'''</span></div>
 
| rowspan="1" colspan="2" |
 
| rowspan="1" colspan="2" |
−
<div>Activates ''moving mode'' by making the moving icons available. The moving icons or the icons that display direction arrows let you move the adjusted image in one direction only by a specified number of pixels. The default number of pixels is 1; however, the number of pixels may be from 0.01 to 2048.0. Therefore, the direction arrows provide the greatest specificity in moving the image, which is perfect for fine adjustments. </div><div>To change the number of pixels, click the Set pixel increment icon; enter a desired number in the Pixel Increment box; and then click Apply. Refer to [Manual2DSeriesOV.html#wp1856133 "Moving and rotating the adjusted image" ]. </div>
+
<div class="CellBody">Commits the changes that you made to the images, but it leaves the window open for you to make further changes if desired.</div>
 
|-
 
|-
 
|
 
|
−
<div>[[Image:RotateIco.jpg]] Rotate Image </div>
+
<div class="CellBody">[[Image:IconSetPixelIncrement.jpg]] <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Set pixel increment</font>'''</span></div>
 
| rowspan="1" colspan="2" |
 
| rowspan="1" colspan="2" |
−
<div>Activates ''rotation mode''. If the rotation of the adjusted image is incorrect, you can change the rotation of the image with the two rotation icons: Rotate clockwise and Rotate counterclockwise. Rotation icons allow you to turn the adjusted image in the desired direction only by a specified degree (1-360). The default degree is 1, and it is shown next to the Rotate Image icon. To change the degree, click the Change Degree Increment icon; enter a desired number in the Degree Increment box; and then click Apply. Refer to [Manual2DSeriesOV.html#wp1856133 "Moving and rotating the adjusted image" ] </div>
+
<div class="CellBody">Determines the number of pixels to use when any of the move image icons are used. When you click this icon, the Change Pixel Increment dialog box opens.
 
|-
 
|-
−
| rowspan="1" colspan="3" |
+
| [[Image:dialogboxChangePixelIncrement.jpg]]
−
<div>'''Figure 8. The Blended tab options ''' </div>
+
|Although the default is 1.0, when the pixel increment is changed to another number, that number displays on the toolbar rather than 1.0. For example, if you changed the pixel increment to 550.0, this number would appear in the icon on the toolbar. You can use any pixel increment from 0.01 to 2048.00.
−
|}
+
−
 
+
−
</div>
+
−
 
+
−
==== Moving and rotating the adjusted image ====
+
−
 
+
−
[Manual2DSeriesOV.html#wp1859991 Figure 9] shows the icons which allow you to move the adjusted image in all directions or specifically up, down, left, and right a certain number of pixels. You can also rotate the adjusted image clockwise or counterclockwise. Note that all these tools are available only on the Blended tab.
+
−
 
+
−
''To activate moving mode'', click on the Translate image icon first, and then use the arrow icons to move the adjusted image in desired direction. You can also set up the moving increment (in pixels). Current increment is shown next to the Translate image icon. Refer to [Manual2DSeriesOV.html#wp1859991 Figure 9].
+
−
 
+
−
''To activate rotation mode'', click on the Rotate Image icon, and then use the Rotate Clockwise or Rotate Counterclockwise icons to rotate the image. You can also set up the rotation increment (in grades). Current increment is shown next to the Rotate Image icon.
+
−
 
+
−
{| border="1" cellpadding="5"
+
−
|+ <div>'''Figure 9. The Blended tab: activating moving and rotation modes''' </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 size="2pt"><font color="#000000"><div><center>[[Image:ImageMovingAndRotation.jpg]]</center></div><br /> </font></font></div>
+
<div class="CellBody">[[Image:IconTranslateImage.jpg]] <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Translate image</font>'''</span></div>
−
|}
+
| rowspan="1" colspan="2" |
−
 
+
<div class="CellBody">Moves Image B, the image to be registered, in any direction you drag the image by the number of pixels indicated in the Set Pixel Increment icon. </div>
−
==== Moving the adjusted image ====
+
−
 
+
−
The Translate image icon activates moving mode for the adjusted image and allows you to move the image in any direction. This icon only appears on the Blended tab, which is where all manual adjustments to image registration occurs. To move the adjusted image, click Translate Image and, holding down the left mouse button, drag the icon in the direction in which you wish to move the image, and then release the mouse button. After a few moments, the image appears in the new position. Note that, depending on where you moved the adjusted image, its outer portions may disappear beyond the outer edges of the reference image. In this case, you can use the same icon to move the adjusted image again.
+
−
 
+
−
==== Moving the adjusted image with the direction arrows ====
+
−
 
+
−
The icons that display direction arrows let you move the adjusted image in one direction only by a specified number of pixels. The default number of pixels is 1; however, the number of pixels may be from 0.01 to 2048.0. Therefore, the direction arrows provide the greatest specificity in moving the image, which is perfect for fine adjustments.
+
−
 
+
−
To change the number of pixels, click the Set pixel increment icon; enter a number in the Pixel Increment box; and then click Apply. See [Manual2DSeriesOV.html#wp1859991 Figure 9].
+
−
 
+
−
==== Rotating the adjusted image ====
+
−
 
+
−
If the rotation of the adjusted image is incorrect, you can change the rotation of the image using the rotation icons as shown in as shown in [Manual2DSeriesOV.html#wp1857728 Figure 10].
+
−
 
+
−
# To activate rotation mode, click the Rotate Image icon.
+
−
# Then, use the Set Degree Increment option to set up the desired degree increment. The increment's range is between 0.01 and 360.0 degrees.
+
−
# Select the center of rotation for the image. In order to do that, click Rotate Image, and then set the center by clicking with the mouse on the image. The letter ''C'' appears with a yellow crosshair cursor ('' ''). You can then drag a line from the center of rotation to move the image above or below the center of rotation.
+
−
# To rotate the image clockwise, click Rotate Clockwise; and to rotate the image counterclockwise, click Rotate Counterclockwise.
+
−
 
+
−
The image can also be rotated manually by dragging away from the center of rotation, and then dragging either clockwise of counterclockwise.
+
−
 
+
−
<div>
+
−
 
+
−
{| border="1" cellpadding="5"
+
−
|+ <div>'''Figure 10. Rotating the adjusted image.''' </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 size="2pt"><font color="#000000"><div><center>[[Image:CenterOfRotation.jpg]]</center></div><br /> </font></font></div>
+
<div class="CellBody">[[Image:IconMoveImageUp.jpg]] <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Move image up</font>'''</span></div>
−
|}
+
| rowspan="1" colspan="2" |
−
 
+
<div class="CellBody">Moves Image B, the image to be registered, up by the number of pixels indicated in the Set Pixel Increment icon.</div>
−
</div>
+
−
 
+
−
{| width="90%" border="1" frame="hsides" frame="hsides"
+
 
|-
 
|-
−
| width="9%" valign="top" |
+
|
−
[[Image:noteicon.gif]]
+
<div class="CellBody">[[Image:IconMoveImageDown.jpg]] <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Move image down</font>'''</span></div>
−
| width="81%" bgcolor="#B0E0E6" | '''Note:''' You can change the degree increment any time to achieve exact registration.
+
| rowspan="1" colspan="2" |
−
|}
+
<div class="CellBody">Moves Image B, the image to be registered, down by the number of pixels indicated in the Set Pixel Increment icon.</div>
−
 
+
−
<br />
+
−
 
+
−
==== Dual tab ====
+
−
 
+
−
The Dual tab shows both the reference image and the adjusted image side by side in the image area at the bottom of the page.
+
−
 
+
−
Note that the border around the reference image, the image on the left side of the page, appears in red. The border around the adjusted image, which is on the right side of the page, appears in green. Several of the icons near the top of the page are color coded to the images. That is, the red icons apply to the reference image, and the green icons apply to the adjusted image.
+
−
 
+
−
==== The Dual tab offers the following options ====
+
−
 
+
−
<div>
+
−
 
+
−
{| border="1" cellpadding="5"
+
−
|+
+
 
|-
 
|-
 
|
 
|
−
<div>'''Blended tab''' </div>
+
<div class="CellBody">[[Image:IconMoveImageRight.jpg]] <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Move image right</font>'''</span></div>
 
| rowspan="1" colspan="2" |
 
| rowspan="1" colspan="2" |
−
<div>Displays the Blended page, which shows the image to be registered superimposed on the reference image. This page allows you to move and align the image to be registered with the reference image. For the Blended tab options refer to [Manual2DSeriesOV.html#wp1847549 Figure 7]. </div>
+
<div class="CellBody">Moves Image B, the image to be registered, right by the number of pixels indicated in the Set Pixel Increment icon.</div>
 
|-
 
|-
 
|
 
|
−
<div>'''Dual tab''' </div>
+
<div class="CellBody">[[Image:IconMoveImageLeft.jpg]] <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Move image left</font>'''</span></div>
 
| rowspan="1" colspan="2" |
 
| rowspan="1" colspan="2" |
−
<div>Displays the Dual page, which shows each image side by side, and allows you to delineate three or more landmarks on each image before you apply the Landmark-Least Squares algorithm or the Landmark-Thin Plate Spline algorithm to the images. </div>
+
<div class="CellBody">Moves Image B, the image to be registered, left by the number of pixels indicated in the Set Pixel Increment icon.</div>
 
|-
 
|-
 
|
 
|
−
<div>[[Image:LUTIco.jpg]] '''Lookup Table''' </div>
+
<div class="CellBody">[[Image:dialogboxChangeDegreeIncrement.jpg]] <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Set degree increment</font>'''</span></div>
 
| rowspan="1" colspan="2" |
 
| rowspan="1" colspan="2" |
−
<div>Displays the Lookup Table window, which includes two tabs: Image A, the reference image, and Image B, the image to be registered. </div>
+
<div class="CellBody"> Determines the degree to use when rotating images, rotating images clockwise, or rotating images counterclockwise. When you click this icon, the Change Degree Increment dialog box opens. Although the default degree increment is 1.0, when the degree increment is changed to another degree, that degree increment displays on the toolbar rather than 1.0. For example, if you changed the degree increment to 180.0, [[Image:IconDegree180.jpg]] would appear on the toolbar. You can set the degree increment from 0.01 to 360.0. </div>
 
|-
 
|-
 
|
 
|
−
<div>[[Image:MagnifyReference.jpg]] '''Magnify reference image 2.0x''' </div>
+
<div class="CellBody">[[Image:IconRotateImage.jpg]] <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Rotate image</font>'''</span></div>
 
| rowspan="1" colspan="2" |
 
| rowspan="1" colspan="2" |
−
<div>Doubles the size of reference images, magnifying them to twice their current size. If an image is too large for the current window size, scroll bars appear, and you may need to manually adjust the size of the window. </div><div>To restore reference images to their original size, use the Magnify Reference Image 0.5x icon, as many times as you used this icon. </div>
+
<div class="CellBody">Allows you to select a center of rotation by clicking on the image with the mouse. It then allows you to then move the image above or below the center of rotation by dragging a line from the center of rotation.</div>
 
|-
 
|-
 
|
 
|
−
<div>[[Image:MinifyReference20.jpg]] '''Magnify reference image 0.5x''' </div>
+
<div class="CellBody">[[Image:IconRotateClockwise.jpg]] <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Rotate clockwise</font>'''</span></div>
 
| rowspan="1" colspan="2" |
 
| rowspan="1" colspan="2" |
−
<div>Reduces the magnification level of reference images in half. To restore reference images to their original size, use the Magnify Reference Image 2.0x icon, as many times as you used this icon. </div>
+
<div class="CellBody">Rotates the image to be registered clockwise by the number of degrees indicated as the degree increment. To restore the image to its original rotation, click [[Image:IconReset.jpg]] , the Reset image to original state icon.</div>
 
|-
 
|-
 
|
 
|
−
<div>[[Image:MagnifyAdjusted.jpg]]''' Magnify adjusted image 2.0x''' </div>
+
<div class="CellBody">[[Image:IconRotateCounterClockwise.jpg]] <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Rotate counterclockwise</font>'''</span></div>
 
| rowspan="1" colspan="2" |
 
| rowspan="1" colspan="2" |
−
<div>Doubles the size of adjusted images, magnifying them to twice their current size. If an image is too large for the current window size, scroll bars appear, and you may need to manually adjust the size of the window. </div><div>To restore adjusted images to their original size, use the Magnify Reference Image 0.5x icon, as many times as you used this icon. </div>
+
<div class="CellBody">Rotates the image to be registered counterclockwise by the number of degrees incited as the degree increment. To restore the image to its original rotation, click [[Image:IconReset.jpg]] , the Reset image to original state icon.</div>
 
|-
 
|-
 
|
 
|
−
<div>[[Image:MinifyAdjusted.jpg]] '''Magnify adjusted image 0.5x''' </div>
+
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Image area</font>'''</span></div>
 
| rowspan="1" colspan="2" |
 
| rowspan="1" colspan="2" |
−
<div>Reduces the magnification level of adjusted images in half. To restore adjusted images to their original size, use the Magnify Reference Image 2.0x icon as many times as you used this icon. </div>
+
<div class="CellBody">Superimposes the image to be registered on the reference image and allows for the image to be registered to be moved, magnified, or rotated.</div>
 +
|}
 +
 
 +
=== Manual 2D Series: Dual tab ===
 +
 
 +
{| 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 6. Manual 2D Series window showing the Dual page <br /></font>'''</div>
 +
|-
 +
|<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Show VOIs in blended window</font>'''</span></div>
 +
|
 +
<div class="CellBody">Displays, on the Blended page, the VOIs that you delineated on the Dual page.</div>
 
|-
 
|-
 
|
 
|
−
<div>[[Image:LeastSquaresIco.jpg]] '''Apply least squares alignment''' </div>
+
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Blended tab</font>'''</span></div>
 
| rowspan="1" colspan="2" |
 
| rowspan="1" colspan="2" |
−
<div>Applies the Landmark-Least Squares algorithm to the image to be registered. After the algorithm is applied, if needed, you can apply the Landmark-Thin Plate Splines algorithm on the image, or you can manually adjust the alignment of the image on the Blended page. </div>
+
<div class="CellBody">Displays the Blended page, which shows the image to be registered superimposed on the reference image. This page allows you to move and align the image to be registered with the reference image.</div>
 
|-
 
|-
 
|
 
|
−
<div>'''[[Image:TPS_ico.jpg]] Apply thin plate spline alignment''' </div>
+
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Dual tab</font>'''</span></div>
 
| rowspan="1" colspan="2" |
 
| rowspan="1" colspan="2" |
−
<div>Applies the Landmark-Thin Plate Spline algorithm to the image to be registered. After this algorithm is applied, if needed, you can apply the Landmark-Least Squares algorithm on the image, or you can manually adjust the alignment of the image on the Blended page. </div>
+
<div class="CellBody">Displays the Dual page, which shows each image side by side, and allows you to delineate three or more landmarks on each image before you apply the Landmark-Least Squares algorithm or the Landmark-Thin Plate Spline algorithm to the images.</div>
 
|-
 
|-
 
|
 
|
−
<div>[[Image:ResetOriginal.jpg]] '''Reset image to original state''' </div>
+
<div class="CellBody">[[Image:IconLookupTable.jpg]] <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Lookup Table</font>'''</span></div>
 
| rowspan="1" colspan="2" |
 
| rowspan="1" colspan="2" |
−
<div>Restores the image to its original state. This icon deletes all points on the reference image and on the adjusted image.''' '''If the Apply button has already been selected, the Reset icon undoes all changes that occurred since the last time the Apply button was selected.  </div>
+
<div class="CellBody">Displays the Lookup Table window, which includes two tabs: Image A, the reference image, and Image B, the image to be registered.</div>
 
|-
 
|-
 
|
 
|
−
<div>[[Image:AddlanmarkRef.jpg]] '''Reference slice markers''' </div>
+
<div class="CellBody">[[Image:IconMagnifyReferenceImageto2.0x.jpg]] <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Magnify reference image 2.0x</font>'''</span></div>
 
| rowspan="1" colspan="2" |
 
| rowspan="1" colspan="2" |
−
<div>Adds a landmark point to the reference image each time you click the left mouse button. Note that the points are sequentially labeled from 1 on in the order in which you created them. To remove points, return the cursor to its default mode by clicking [Manual2DSeriesOV.html#wp1855768 ''Return to default mode''], select the point to be deleted, and then click the Delete Selected Reference Slice Markers icon. </div>
+
<div class="CellBody">Doubles the size of reference images, magnifying them to twice their current size. If an image is too large for the current window size, scroll bars appear, and you may need to manually adjust the size of the window.</div> <div class="CellBody">To restore reference images to their original size, use [[Image:IconMagnifyReferenceImageto0.5x.jpg]] , the Magnify reference image 0.5x icon, as many times as you used this icon.</div>
 
|-
 
|-
 
|
 
|
−
<div>'''[[Image:AddLandmarkAdjusted.jpg]] Adjusted slice markers''' </div>
+
<div class="CellBody">[[Image:IconMagnifyReferenceImageto0.5x.jpg]] <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Magnify reference image 0.5x</font>'''</span></div>
 
| rowspan="1" colspan="2" |
 
| rowspan="1" colspan="2" |
−
<div>Adds a landmark point to the adjusted image each time you click the left mouse button. Note that the points are sequentially labeled from 1 to n in the order in which you created them. To remove points, return the cursor to its default mode by clicking [Manual2DSeriesOV.html#wp1855768 ''Return to default mode''], select the point to be deleted, and click the Delete Selected Adjusted Slice Markers icon. '''Note:''' landmarks in the reference image should correspond to landmarks in the adjusted image. </div>
+
<div class="CellBody">Reduces the magnification level of reference images in half. To restore reference images to their original size, use [[Image:IconMagnifyReferenceImageto2.0x.jpg]] , the Magnify reference image 2.0x icon, as many times as you used this icon.</div>
 
|-
 
|-
 
|
 
|
−
<div>'''[[Image:RemoveLandmarkRef.jpg]] Delete selected reference slice markers''' </div>
+
<div class="CellBody">[[Image:IconMagnifyAdjustedImage 2.0x.jpg]] <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Magnify adjusted image 2.0x</font>'''</span></div>
 
| rowspan="1" colspan="2" |
 
| rowspan="1" colspan="2" |
−
<div>Removes the landmark point that you selected in the reference image. To remove a point, first return the cursor to its default mode by clicking [Manual2DSeriesOV.html#wp1855768 ''Return to default mode''], then select the point to be deleted, and then click the Delete Selected Reference Slice Markers icon. </div>
+
<div class="CellBody">Doubles the size of adjusted images, magnifying them to twice their current size. If an image is too large for the current window size, scroll bars appear, and you may need to manually adjust the size of the window.</div> <div class="CellBody">To restore adjusted images to their original size, use [[Image:IconMagnifyAdjustedImage 0.5x.jpg]] , the Magnify reference image 0.5x icon, as many times as you used this icon.</div>
 
|-
 
|-
 
|
 
|
−
<div>'''[[Image:RemoveLandmarkAdj.jpg]] Delete selected adjusted slice markers''' </div>
+
<div class="CellBody">[[Image:IconMagnifyAdjustedImage 0.5x.jpg]] <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Magnify adjusted image 0.5x</font>'''</span></div>
 
| rowspan="1" colspan="2" |
 
| rowspan="1" colspan="2" |
−
<div>Removes the landmark point that you selected in the adjusted image. To remove the point, first return the cursor to its default mode by clicking [Manual2DSeriesOV.html#wp1855768 ''Return to default mode''], then select the point to be deleted, and finally click the Delete Selected Adjusted Slice Markers icon. </div>
+
<div class="CellBody">Reduces the magnification level of adjusted images in half. To restore adjusted images to their original size, use [[Image:IconMagnifyAdjustedImage 2.0x.jpg]] , the Magnify reference image 2.0x icon, as many times as you used this icon.</div>
 
|-
 
|-
 
|
 
|
−
<div>[[Image:ReferenceToAdjusted.jpg]]Copy reference markers to adjusted image </div>
+
<div class="CellBody">[[Image:IconLeastSquaresAlignment.jpg]] <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Apply least squares alignment</font>'''</span></div>
 
| rowspan="1" colspan="2" |
 
| rowspan="1" colspan="2" |
−
<div>Copies landmarks from the reference image to adjusted image. Note that landmarks which were copied to the adjusted image have the same ''x, y'' coordinates as the reference image landmarks. </div>
+
<div class="CellBody">Applies the Landmark-Least Squares algorithm to the image to be registered. After the algorithm is applied, if needed, you can apply the Landmark-Thin Plate Splines algorithm on the image, or you can manually adjust the alignment of the image on the Blended page.</div>
 
|-
 
|-
 
|
 
|
−
<div>[[Image:AdjustedToReferenceIco.jpg]]Copy adjusted markers to reference markers </div>
+
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">[[Image:IconThinPlateSplineAlignment.jpg]] Apply thin plate spline alignment</font>'''</span></div>
 
| rowspan="1" colspan="2" |
 
| rowspan="1" colspan="2" |
−
<div>Copies landmarks from the adjusted image to reference image. Note that landmarks you copied to the reference image have the same ''x, y'' coordinates as the adjusted image landmarks. </div>
+
<div class="CellBody">Applies the Landmark-Thin Plate Spline algorithm to the image to be registered. After this algorithm is applied, if needed, you can apply the Landmark-Least Squares algorithm on the image, or you can manually adjust the alignment of the image on the Blended page.</div>
 
|-
 
|-
 
|
 
|
−
<div>'''[[Image:ReturnToDefaultMode.jpg]] Return to default mode''' </div>
+
<div class="CellBody">[[Image:IconReset.jpg]] <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Reset image to original state</font>'''</span></div>
 
| rowspan="1" colspan="2" |
 
| rowspan="1" colspan="2" |
−
<div>'''Returns the cursor to its default mode, which allows you to change from adding points to deleting points from the image.''' </div>
+
<div class="CellBody">Restores the image to be registered to its original state. Restores image to its original state. This icon deletes all points on the reference image and on the image to be registered.<span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000"> </font>'''</span>If the Apply button has already been selected, the Reset icon undoes all changes that occurred since the last time the Apply button was selected. </div>
 
|-
 
|-
 
|
 
|
−
<div>[[Image:btnApply.jpg]] '''Apply ''' </div>
+
<div class="CellBody">[[Image:IconReferenceSliceMarkers.jpg]] <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Reference slice markers</font>'''</span></div>
 
| rowspan="1" colspan="2" |
 
| rowspan="1" colspan="2" |
−
<div>Commits the changes that you made to the images, but it leaves the window open for you to make further changes if desired. </div>
+
<div class="CellBody">Adds a point to the reference image each time you click the left mouse button. Note that the points are sequentially labeled from 1 on in the order in which you created them. To remove points, return the cursor to its default mode by clicking <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">[[Image:IconReturntoDefaultMode.jpg]] </font>'''</span>, select the point to be deleted, and click [[Image:IconDeleteSelectedReferenceSliceMarkers.jpg]] , Delete selected reference slice markers.</div>
−
|-
+
−
| rowspan="1" colspan="3" |
+
−
<div>'''Figure 11. The Dual tab options ''' </div>
+
−
|}
+
−
 
+
−
</div><div>
+
−
 
+
−
{| border="1" cellpadding="5"
+
−
|+ <div>'''Figure 12. The Dual tab shows both: the reference image and adjusted image side by side. Three corresponding landmark points were delineated in the reference and adjusted image.''' </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 size="2pt"><font color="#000000"><div><center>[[Image:DualTab2.jpg]]</center></div><br /> </font></font></div>
+
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">[[Image:IconAdjustedSliceMarkers.jpg]] Adjusted slice markers</font>'''</span></div>
−
|}
+
| rowspan="1" colspan="2" |
−
 
+
<div class="CellBody">Adds a point to the adjusted image each time you click the left mouse button. Note that the points are sequentially labeled from 1 on in the order in which you created them. To remove points, return the cursor to its default mode by clicking <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">[[Image:IconReturntoDefaultMode.jpg]] </font>'''</span>, select the point to be deleted, and click [[Image:IconDeleteSelectedAdjustedSliceMarkers.jpg]] , Delete selected adjusted slice markers.</div>
−
</div>
+
−
 
+
−
==== Using the image registration algorithms ====
+
−
 
+
−
Before applying the Landmark-Least Squares algorithm or the Landmark-Thin Plate Spline algorithm to the images you must delineate three or more ''landmark points'' or ''landmarks'' on each image. See [Manual2DSeriesOV.html#wp1856529 Figure 12].
+
−
 
+
−
==== Delineating the landmark points ====
+
−
 
+
−
''To place landmarks on the reference image'', click the Reference Slice Markers icon, and then click the mouse on the reference image where the landmark should be located. The landmark appears on the image in red type and is sequentially numbered. Create at least two more landmarks on the image.
+
−
 
+
−
''To place landmarks on the adjusted image'', click the Adjusted Slice Markers icon, and create at least three landmarks on the image by clicking the mouse. The landmarks, which are sequentially numbered, appear in green type.
+
−
 
+
−
''To remove a landmark point'' from the reference or adjusted image, you need to return the mouse cursor to its default mode by clicking on the Return to Default Mode icon. You can then select the point by clicking on it with the mouse, and then delete it by clicking the corresponding Delete Selected Markers icon.
+
−
 
+
−
==== Applying the image registration algorithms ====
+
−
 
+
−
After you have delineated the landmark points on both images, select the Least Squares algorithm. <font>'''The Least Squares algorithm'''</font><font> registers the adjusted image to the reference image by using corresponding points placed in both images.</font>
+
−
 
+
−
''The Thin Plate Spline algorithm'' allows you to register two images in a nonlinear manner using the corresponding landmark points that you delineate in both images.
+
−
 
+
−
The program registers the images and the landmarks appear in yellow type followed by the specific positions in parentheses.
+
−
 
+
−
At this point, you should determine the following:
+
−
 
+
−
# Whether there is a need to make other manual adjustments to the registration. If so, return to the Blended tab and use the direction or the rotation icons. Use the ''Window region of image B ''icon to verify alignment. Refer to [Manual2DSeriesOV.html#wp1846463 "making manual reconcilements to the adjusted image" ].
+
−
# Whether to run the other algorithm. If so, simply call either the Least Squares or Thin Plate Spline algorithm, as appropriate.
+
−
# Whether to restore the adjusted image to its original form by clicking Reset.
+
−
# Whether to select Apply to keep changes made by the algorithm.
+
−
 
+
−
==== making manual reconcilements to the adjusted image ====
+
−
 
+
−
After you apply either the Least Squares or the Thin Plate Spline algorithm on the images, you may want to manually ascertain whether key portions of the reference image and the image to be registered, or adjusted image, are in alignment. One way of checking alignment, or registration, is using the ''Window region of image B ''icon''. ''A recommended method for checking registration and for correcting it follows.
+
−
 
+
−
To check registration, do the following:
+
−
 
+
−
# Click Blended in the Manual 2D Series window to display the Blended page. Both the reference image and the image to be registered, or adjusted image, appear at the bottom of the window. The adjusted image is superimposed over the reference image.
+
−
# By default, the arrow on the AlphaBlending slider appears in the middle of the slider at 0.5R/A, which means that 50 percent of each image are shown on the page.
+
−
# Slide the arrow on the AlphaBlending slider all the way to the right until it reaches the label "Adj. A." This label indicates that 100 percent of the adjusted image is displayed on the page and, therefore, the reference image does not appear.
+
−
# Now, open Lookup table for the adjusted image. Note that the window includes two tabs: one for Image A, the reference image, and one for Image B, the adjusted image.
+
−
# Use the LUT options to change the intensity for one of the color channels for the adjusted image, for example, to increase the red channel. The purpose in doing this task is to easily distinguish the adjusted image from the reference image. Refer to [Manual2DSeriesOV.html#wp1866423 "Using LUT to arrange the images" ].
+
−
# Return to the Blended tab of Manual 2D Registration dialog box and move the AlphaBlending Image slider arrow all the way to the left on the slider. The label "Ref. R" indicates that the page now displays 100 percent of the reference and does not display the adjusted image.
+
−
# Click the Window Region of Image B'' ''icon and position the cursor over the reference image. Notice that a square box appears on the image. The box is filled with the adjusted image, which is appears in pale red. You can use this box to look at the alignment of details in the images. See [Manual2DSeriesOV.html#wp1864075 Figure 13].
+
−
 
+
−
<div>
+
−
 
+
−
{| border="1" cellpadding="5"
+
−
|+ <div>'''Figure 13. The Window Region box is filled with the adjusted image''' </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 size="2pt"><font color="#000000"><div><center>[[Image:WindowRegionRed.jpg]]</center></div><br /> </font></font></div>
+
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">[[Image:IconDeleteSelectedReferenceSliceMarkers.jpg]] Delete selected reference slice markers</font>'''</span></div>
−
|}
+
| rowspan="1" colspan="2" |
−
 
+
<div class="CellBody">Removes the point that you selected in the reference image. To remove a point, first return the cursor to its default mode by clicking <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">[[Image:IconReturntoDefaultMode.jpg]] </font>'''</span>, select the point to be deleted, and click <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">[[Image:IconDeleteSelectedReferenceSliceMarkers.jpg]] </font>'''</span>, Delete selected reference slice markers.</div>
−
</div>
+
−
 
+
−
# Determine whether you want to correct the alignment of the images. If you do, there are several ways to align the adjusted image:
+
−
# Moving the image using the Translate image icon and direction arrows. See also [Manual2DSeriesOV.html#wp1860034 "Moving the adjusted image" ].
+
−
# Rotating the image using the Rotate Image icon. See also [Manual2DSeriesOV.html#wp1862562 "Rotating the adjusted image" ].
+
−
 
+
−
==== Using LUT to arrange the images ====
+
−
 
+
−
You can use the LUT options to distinguish the adjusted image from the reference image. In order to to that
+
−
 
+
−
# Return to Blended mode.
+
−
# Click the Lookup Table icon, to display the Lookup Table window. Note that the window includes two tabs: one for Image A - the reference image, and the other one for Image B - the adjusted image.
+
−
# For the adjusted image, drag the image intensity line for the red channel up in the middle. In this case, it creates a lighter colored red. The adjusted image now appears in pale red. Actually, you can change the color of the image to any color. See [Manual2DSeriesOV.html#wp1864378 Figure 14] below.
+
−
 
+
−
<div><br /> </div><div>
+
−
 
+
−
{| border="1" cellpadding="5"
+
−
|+ <div>'''Figure 14. The adjusted image and its Lookup table''' </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 size="2pt"><font color="#000000"><div><center>[[Image:AdjustedImageLUT.jpg]]</center></div><br /> </font></font></div>
+
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">[[Image:IconDeleteSelectedAdjustedSliceMarkers.jpg]] Delete selected adjusted slice markers</font>'''</span></div>
−
|}
+
| rowspan="1" colspan="2" |
−
 
+
<div class="CellBody">Removes the point that you selected in the image to be registered. To remove a point, first return the cursor to its default mode by clicking <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">[[Image:IconReturntoDefaultMode.jpg]] </font>'''</span>, select the point to be deleted, and click <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">[[Image:IconDeleteSelectedAdjustedSliceMarkers.jpg]] </font>'''</span>, Delete selected adjusted slice markers.</div>
−
</div>
+
−
 
+
−
{| width="90%" border="1" frame="hsides" frame="hsides"
+
−
|-
+
−
| width="9%" valign="top" |
+
−
[[Image:tipicon.gif]]
+
−
| width="81%" bgcolor="#B0E0E6" | '''Tip:'''You may want to maximize the window and enlarge the images so that you can view details of the images while checking alignment. To maximize the window, simply click Restore. To maximize the image, click the Magnify image 2.0x icon, which magnifies the image to twice its current size, as many times as needed.
+
−
|}
+
−
 
+
−
<br />
+
−
 
+
−
# Return to the Blended tab and move the image slider arrow all the way to the left on the slider, so the page now displays only the reference image.
+
−
# Click the Window Region of Image B'' ''icon and position the cursor over the reference image.
+
−
# The Windows Region box appears on the image, filled with the adjusted image, which is appears in pale red.
+
−
# Use this box to look at the alignment of details in the images.
+
−
 
+
−
<div>
+
−
 
+
−
{| border="1" cellpadding="5"
+
−
|+ <div>'''Figure 15. The adjusted image which appears in the Blended tab and also in the Window Region.''' </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 size="2pt"><font color="#000000"><div><center>[[Image:RedAdjustedImage2.jpg]]</center></div><br /> </font></font></div>
+
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">[[Image:IconReturntoDefaultMode.jpg]] Return to default mode</font>'''</span></div>
−
|}
+
| rowspan="1" colspan="2" |
−
 
+
<div class="CellBody"><span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">Returns the cursor to its default mode, which allows you to change from adding points to deleting points from the image.</font></span></div>
−
</div>
+
−
 
+
−
=== Applying the Manual 2D Series algorithm to 2.5D images ===
+
−
 
+
−
To run this algorithm on 2.5D images, complete the following steps:
+
−
 
+
−
# Open a single 2.5 image dataset. When you apply this algorithm, you select the slices in the dataset that you want to register.
+
−
# Perform, as an option, any other image processing, except scaling, on the image dataset.
+
−
# Select Algorithms &gt; Registration &gt; Manual 2D Series. The Manual 2D Series window for 2.5D images ([Manual2DSeriesOV.html#wp1866286 Figure 16]) opens.
+
−
# Because you are registering slices of the image, and not separate images, all of the necessary icons and controls appear in a simple window that does not include tabbed pages. Note that two additional sliders appear at the top of the page:
+
−
#* ''Reference slice slider'' allows you to choose which slice to use as a reference image.
+
−
#* ''Adjusted slice slider'''' ''allows you to choose which slice to use as an image to be registered.
+
−
 
+
−
{| width="90%" border="1" frame="hsides" frame="hsides"
+
−
|-
+
−
| width="9%" valign="top" |
+
−
[[Image:noteicon.gif]]
+
−
| width="81%" bgcolor="#B0E0E6" | '''Note:''' the boxes to the right of each slider indicate the number of slice which you are currently viewing. All of the remaining icons and controls work in the same way that they do on the Manual 2D Series window for 2D images.
+
−
|}
+
−
 
+
−
<br />
+
−
 
+
−
# Choose the reference and adjusted slice. You can consider using the LUT to distinguish the adjusted image from the reference image as described in Section [Manual2DSeriesOV.html#wp1866423 "Using LUT to arrange the images" ].
+
−
# Use the Alphablending image slider to display only the reference slice and then place at least four landmarks on the reference slice. Repeat the same procedure for the adjusted slice.
+
−
# Now, move the image slider arrow all the way to the left on the slider, so the dialog box will display only the reference slice.
+
−
# Click the Window Region of Image B'' ''icon and position the cursor over the reference image. The Windows Region box appears on the image, filled with the adjusted image, as shown in [Manual2DSeriesOV.html#wp1866286 Figure 16]. Use this box to look at alignment of fine detail in the slices.
+
−
 
+
−
<div>
+
−
 
+
−
{| border="1" cellpadding="5"
+
−
|+ <div>'''Figure 16. Applying the Manual 2D Series Registration algorithm on a 2.5D image. Slice 3 (adjusted slice) is registered to slice 1 (reference slice). To differentiate the slices, we use LUT options to color the reference slice to pale green and adjusted slice to pale blue.''' </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 size="2pt"><font color="#000000"><div><center>[[Image:Manual25DRegistration.jpg]]</center></div><br /> </font></font></div>
+
<div class="CellBody">[[Image:BtnApply.jpg]] <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Apply </font>'''</span></div>
 +
| rowspan="1" colspan="2" |
 +
<div class="CellBody">Commits the changes that you made to the images, but it leaves the window open for you to make further changes if desired.</div>
 
|}
 
|}
  
−
</div>
+
<div id="Applying25D"><div>
 +
== Applying the Manual 2D Series algorithm on 2.5 images ==
  
−
# At this point, you should determine the following:
+
<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"> To run this algorithm on 2.5D images, complete the following steps:<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 a single 2.5 image dataset. When you apply this algorithm, you select the slices in the dataset that you want to register.<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 Perform, as an option, any other image processing, except scaling, on the image dataset.<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 Algorithms &gt; Registration &gt; Manual 2D Series. The Manual 2D Series window for 2.5D images (see Figure 7]) 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: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> Because you are registering slices of an image, and not separate images, all of the necessary icons and controls appear in a simple window that does not include tabbed pages. Note that there are two sliders at the top of the page:<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-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">Reference slice slider</font>''</span>-Allows you to choose which slice to use as a reference image. <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-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">Adjusted slice slider</font>''</span>-Allows you to choose which slice to use as an image to be registered. <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 boxes to the right of each slider indicate which slice you are currently viewing. <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"> All of the remaining icons and controls work in the same way that they do on the Manual 2D Series window for 2D images (refer to Figure 5 and Figure 6).<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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#* Whether there is a need to make manual adjustments to the registration. If so, use the direction or the rotation icons to verify alignment.
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#* Whether to run one of the registration algorithms. If so, simply call either the Least Squares or Thin Plate Spline algorithm, as appropriate. Select Apply to keep changes made by the algorithm.
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=== Applying the Manual 2D Series algorithm to 3D images ===
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For 2.5D images, the algorithm's window does not include the Blended and Dual tabbed pages. Rather is incorporates some of the same interface controls that appear on the Blended and Dual pages, such as icons and the alphablending slider. Note that you can place landmarks on the image in this window.
  
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When you apply this algorithm, you select ''the slices, ''which you want to register, in a single 3D dataset. To run the algorithm on 3D images, complete the following steps:
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== References ==
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# Open a single3 image dataset. Perform, as an option, any other image processing, except scaling, on the image dataset.
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# Select Algorithms &gt; Registration &gt; Manual 2D Series. The Manual 2D Series window for 3D images opens.
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# Because you are registering'' slices of a single 3D image'', all of the necessary icons and controls appear in a window that does not include tabs. Note that there are three sliders appear at the top of the page:
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#* ''Reference slice slider'' allows you to choose which slice to use as a reference image.
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#* ''Adjusted slice slider'''' ''allows you to choose which slice to use as an image to be registered.
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#* ''AlphaBlending Slider'' which, by default, displays both the reference and adjusted slices blended in proportion 50/50.
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{| width="90%" border="1" frame="hsides" frame="hsides"
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[[Image:noteicon.gif]]
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| width="81%" bgcolor="#B0E0E6" | '''Note:''' the boxes to the right of the Reference Slice and Adjusted Slice slider indicate the number of slice which you are currently viewing. All of the remaining icons and controls work in the same way that they do on the Manual 2D Series window for 2D images.
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For more information, refer to:
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K.S. Arun, T.S. Huang, and S.D. Blostein, "Least-Squares Fitting of Two 3-D Point Sets" , IEEE Transactions on Pattern Analysis and Machine Intelligence, Vol. PAMI-9, No. 5, September, 1987, pp. 698-700.
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David Eberly, "Thin Plate Splines" of Magic Software at http://www.magic-software.com. Also at the same site are the files: MgcInterp2DThinPlateSpline.h, MgcInterp2DThinPlateSpline.cpp, MgcInterp3DThinPlateSpline.h, MgcInterp3DThinPlateSpline.cpp Paper that explains warping from one <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">x,y</font>''</span> source to another <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">x,y</font>''</span> target set.
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Fred L. BookStein, "Principal Warps: Thin-Plate Splines and the Decompositions of Deformations," IEEE Transactions on Pattern Analysis and Machine Intelligence, Vol. 11, No. 6, June 1989, pp. 567-585.
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# Choose the reference and adjusted slice. Use the LUT to differentiate the adjusted image from the reference image. See also: Section [Manual2DSeriesOV.html#wp1866423 "Using LUT to arrange the images" ].
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[[Category:Help]]
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# Use the AlphaBlending image slider to display only the reference slice and then place at least four landmarks on the reference slice. Repeat the same procedure for the adjusted slice.
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[[Category:Help:Algorithms]]
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# Move the image slider arrow all the way to the left on the slider, so the window now displays only the reference slice.
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# Click the Window Region of Image B'' ''icon and position the cursor over the reference image. The Windows Region box appears on the image, filled with the adjusted image, as shown in [Manual2DSeriesOV.html#wp1867118 Figure 17]. You can use either this box or Checker Board to look at alignment of details in the slices.
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# At this point, you should figure out the following:
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#* Whether there is a need to make further manual adjustments to the registration. If so, use the direction or the rotation icons to verify alignment.
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#* Whether to run one of the registration algorithms. If so, simply call either the Least Squares or Thin Plate Spline algorithm, as appropriate.
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# When done, select Apply to keep changes made by the algorithm.
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<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 size="2pt"><font color="#000000"><div><center>[[Image:Manual3DRegistration.jpg]]</center></div><br /> </font></font></div>
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<div style="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 size="8pt"><font color="#000000">[[Image:TranslateIco.jpg]] Translate Image<br /> </font></font>''</div><div style="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 size="8pt"><font color="#000000">[[Image:RotateIco.jpg]] Rotate Image<br /> </font></font>''</div><div style="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 size="8pt"><font color="#000000">''[[Image:iconMoveImageUp.jpg]]'' Move up<br /> </font></font>''</div><div style="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 size="8pt"><font color="#000000">''[[Image:iconMoveImageRight.jpg]]'' Move right<br /> </font></font>''</div>
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<div style="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 size="8pt"><font color="#000000"> Rotate Image<br /> </font></font>''</div><div style="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 size="8pt"><font color="#000000">''[[Image:iconLeastSquaresAlignment.jpg]]'' Apply Least Squares alignment<br /> </font></font>''</div><div style="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 size="8pt"><font color="#000000">'''[[Image:iconThinPlateSplineAlignment.jpg]]''' Apply Thin Plate Spline alignment<br /> </font></font>''</div><div style="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 size="8pt"><font color="#000000">[[Image:iconReferenceSliceMarkers.jpg]] Reference Slice Markers<br /> </font></font>''</div><div style="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 size="8pt"><font color="#000000">[[Image:iconAdjustedSliceMarkers.jpg]] Adjusted Slice Markers<br /> </font></font>''</div><div style="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 size="8pt"><font color="#000000">[[Image:iconReturntoDefaultMode.jpg]] Return to Default mode<br /> </font></font>''</div><div style="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 size="8pt"><font color="#000000">''[[Image:iconWindowRegionofImageB.jpg]]'' Window region<br /> </font></font>''</div>
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| align="right" | '''<font size="2" color="#800080" face="Verdana">Imaging Sciences Laboratory, CIT, NIH<br /> Matthew McAullife, Ph.D.<br /> mcmatt@exchange.nih.gov<br /> 301-594-2432<br /> Building 12A, Room 2041,<br /> 9000 Rockville Pike, Bethesda, MD 20892</font>'''<br />
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Latest revision as of 19:51, 11 July 2012

The Manual 2D Series algorithm allows you to manually or semimanually register two 2D grayscale or color images by placing corresponding points on both images and then applying either the Landmark-Thin Plate Spline or Landmark-Least Squares algorithm. After applying one of these algorithms, you can then, if needed, use the other algorithm. In addition, at any time, you can manually adjust the alignment of each image.

The algorithm also lets you manually register different slices of a 2.5 image dataset in the same way as the 2D images.

Background

Registration: Manual 2D Series window

Through the Registration: Manual 2D Series window (Figure 1), this algorithm provides the tools for manually registering images and the ability to use two of the landmark registration algorithms. The Registration: Manual 2D Series window includes two tabs: Blended and Dual.

Blended tab

On the Blended page, the window superimposes the image to be registered on top of the reference image. This page includes icons for aligning, rotating, alphablending, and magnifying or minifying the images as well as icons for modifying the lookup table for each image and for applying a checkerboard pattern to assist in alignment.

Dual tab

Clicking the Dual tab opens the Dual page, which displays the images side by side. A number of icons appear in the toolbar. The red icons are color coded to the reference image, which appears on the left and is surrounded by a red border. The green icons apply to the image to be registered, which is shown on the right side of the page and is surrounded by a green border.

The Dual page displays the images side by side

Delineating corresponding points

Before being able to use either the Thin Plate Spline or Least Squares algorithm, you must first delineate a minimum of three corresponding points on both images. These points serve as guides, or landmarks, for aligning the images. In order for the points to be corresponding, you should delineate each point in the same sequence; i.e., the first point that you delineate on the reference image should be the first point delineated on the image to be registered, the second point on the reference image should be the second point delineated on the image to be registered, and so on.

To delete a point, you must first select the point and then use the appropriate Delete icon to delete it. However, before you can select the point, you need to return the cursor to its default mode using the IconReturntoDefaultMode.jpg icon.

On both the Blended and Dual pages, you can modify the lookup table (LUT) by clicking IconLookupTable.jpg , the LUT icon. When you select IconLookupTable.jpg , the Lookup Table window appears. This window includes two tabbed pages: one for Image A, the reference image, and one for Image B, the image to be registered.

A common icon-IconReset.jpg , the Reset icon-appears on both the Blended and Dual pages. Use this icon if you want to restore the original version of the images. This icon deletes all points on the reference image and on the image to be registered.

Note: If the Apply button has already been selected, the Reset icon undoes all changes that occurred since the last time the Apply button was selected.

Image types

You can apply this algorithm to 2D grayscale and color images.

The dimensions or image type of the image to be registered need not be the same as the dimensions or image type of the reference image. The registered image has the same image type as the image to be registered and the same extents as the reference image.

Special notes regarding the number of references points

The following notes apply:

  • For 2D images, three or more points are required. The algorithm may fail if nearly all of the points fall on the same line.
  • For 3D images, four or more points are required and the algorithm may fail if the points nearly all fall on the same plane.
div id="ApplyingOn2D">

Applying the Manual 2D Series algorithm on 2D images

The Load dialog box

1 Open two images: the reference image and the image that you want to register. 2 Select the reference image. 3 Select Algorithms > Registration > Manual 2D Series. The Load dialog box appears. 4 Select the image that you want to register to the reference image. If only two images are open, the Set as Image B box automatically selects the other open image-the one you did not select-as Image B, or the image to be registered. 5 To select a different image, click Browse to find and open another image file. 6 Click OK. The Manual 2D Series window opens.

Note: Opening this window automatically corrects image resolution and scaling. The algorithm window includes two tabs: Blended, which displays the Blended page Dual, which displays the Dual page The Blended page shows both images: the image to be registered superimposed on top of the reference image. Note that the icons near the top of the page allow you to move the image to be registered in all directions or specifically up, down, left, and right a certain number of pixels. You can also rotate the image to be registered clockwise or counterclockwise. 7 Click Dual to go to the Dual page.

The Dual page shows both the reference image and the image to be registered side by side in the image area at the bottom of the page. Note that the border around the reference image, the image on the left side of the page, appears in red. The border around the image to be registered, which is on the right side of the page, appears in green. Several of the icons near the top of the page are color coded to the images. That is, the red icons apply to the reference image, and the green icons apply to the image to be registered.


8 Place at a minimum three landmarks, or points, on each of the images. On the reference image, click IconReferenceSliceMarkers.jpg , the Reference Slice Markers icon, and click the mouse on the reference image where the landmark should be located. The landmark appears on the image in red type and is sequentially numbered. Create at least two more landmarks on the image.

On the image to be registered, click IconAdjustedSliceMarkers.jpg , the Adjusted Slice Markers icon, and creates a landmark on the image by clicking the mouse. The landmark, which is sequentially numbered, appears in green type. Create a minimum of three landmarks on the image.

To delete a point on the reference image, you need to return the cursor to its default mode by clicking on IconReturntoDefaultMode.jpg . You can then select the point by clicking on it with the mouse and then delete it by clicking IconDeleteSelectedReferenceSliceMarkers.jpg , the Delete selected reference slice markers icon.

To delete a point on the image to be registered, or adjusted image, click IconReturntoDefaultMode.jpg , select the point, and then delete it by clicking IconDeleteSelectedAdjustedSliceMarkers.jpg , the Delete adjusted slice markers icon.


9 Select, if desired, either IconLeastSquaresAlignment.jpg , the Least Squares algorithm icon, or IconThinPlateSplineAlignment.jpg , the Thin Plate Spline algorithm, to register the images. The program registers the images and the landmarks appear in yellow type followed by the specific positions in parentheses.

10 At this point, you should determine the following: Whether there is a need to make manual adjustments to the registration. If so, return to the Blended page and use the direction or the rotation icons. Use IconWindowRegionofImageB.jpg to verify alignment (refer to [RegistrationManual2DSeries.html] and to the following tables for more information.

Whether to run the other algorithm. If so, simply click either IconLeastSquaresAlignment.jpg , the Least Squares algorithm, or IconThinPlateSplineAlignment.jpg Thin Plate Spline algorithm, as appropriate.


Whether to restore the image to its original form by clicking IconResetImagetoOriginalState.jpg.

Whether to select Apply to keep changes made by the algorithm.

Making manual adjustments to the image to be registered

After you apply either IconLeastSquaresAlignment.jpg , the Least Squares algorithm icon, or IconThinPlateSplineAlignment.jpg , the Thin Plate Spline algorithm on the images, you may want to manually ascertain whether key portions of the reference image and the image to be registered, or adjusted image, are in alignment. One way of checking alignment, or registration, is using IconWindowRegionofImageB.jpg , the Window region of image B icon. A recommended method for checking registration and for correcting it follows.

Checking registration

To check registration, do the following:

1 Click Blended in the Manual 2D Series window to display the Blended page. Both the reference image and the image to be registered, or adjusted image, appear at the bottom of the window. The adjusted image is superimposed over the reference image. 2 Note that the arrow on the Alphablending slider appears in the middle of the slider at 0.5R/A, which means that 50 percent of each image are shown on the page. 3 Slide the arrow on the Alphablending slider all the way to the right until it reaches the label "Adj. A." This label indicates that 100 percent of the adjusted image is displayed on the page and, therefore, the reference image does not appear.

Note: The label "0.75A" means that 75 percent of the adjusted image appears and only 25 percent of the reference image is displayed.

4 Click IconLookupTable.jpg , the Lookup Table icon, to display the Lookup Table window. Note that the window includes two tabs: one for Image A, the reference image, and one for Image B, the image to be registered.

5 Drag the image intensity line for the red channel up in the middle to adjust the color of the adjusted image. In this case, it creates a lighter colored red. The adjusted image now appears in pale red.

Note: Actually, you can change the color of the image to any color. The purpose in doing this task is to easily distinguish the adjusted image from the reference image. 6 Move the slider arrow all the way to the left on the slider. The label "Ref. R" indicates that the page now displays 100 percent of the reference and does not display the adjusted image. 7 Click IconWindowRegionofImageB.jpg and position the cursor over the reference image. Notice that a square box appears on the image. The box is filled with a red image, which is the adjusted image. You can use this box to look at the alignment of details in the images.

Tip: You may want to maximize the window and enlarge the images so that you can view details of the images while checking alignment. To maximize the window, simply click File:ButtonRestore.jpg , the Restore button. To maximize the image, click the Magnify image 2.0x icon, which magnifies the image to twice its current size, as many times as needed.

8 Determine whether you want to correct the alignment of the images. If you do, there are several ways to move the adjusted image:

  • Moving the image using IconTranslateImage.jpg,the Translate image icon;
  • Moving the image using the direction arrows;
  • Setting the number of pixels to move the image with the Set pixel increment icon;
  • Rotating the image.

Moving the adjusted image in any direction

The Translate image icon, or IconTranslateImage.jpg , allows you to move the adjusted image in any direction. This icon only appears on the Blended page, which is where all manual adjustments to image registration occurs.

To move the adjusted image, click IconTranslateImage.jpg , and, holding down the left mouse button, drag the icon in the direction in which to move the image, and then release the mouse button. After a few moments, the image appears in the new position. Note that, depending on where you moved the adjusted image, its outer portions may disappear beyond the outer edges of the reference image (see Figure 3).). In this case, you can use IconTranslateImage.jpg to move the adjusted image again.


Moving the adjusted image with the direction arrows

The icons that display direction arrows (IconMoveImageUp.jpg , the Move image up icon; IconMoveImageDown.jpg , the Move image down icon; IconMoveImageRight.jpg , the Move image right icon; and IconMoveImageLeft.jpg , the Move image left icon) let you move the adjusted image in one direction only by a specified number of pixels. The default number of pixels is 1; however, the number of pixels may be from 0.01 to 2048.0. Therefore, the direction arrows provide the greatest specificity in moving the image, which is perfect for fine adjustments.

To change the number of pixels, click IconSetPixelIncrement.jpg , the Set pixel increment icon; enter a number in the Pixel Increment box; and click Apply.

Rotating the adjusted image

If the rotation of the adjusted image is incorrect, you can change the rotation of the image with the rotation icons: IconRotateImage.jpg , the Rotate image icon; IconRotateClockwise.jpg , the Rotate clockwise icon; and IconRotateCounterClockwise.jpg , the Rotate counterclockwise icon.

To select the center of rotation for the image, click IconRotateImage.jpg and set the center by clicking with the mouse on the image. The letter C appears with a yellow crosshair cursor (see Figure 4]). You can then drag a line from the center of rotation to move the image above or below the center of rotation. To rotate the image clockwise, click IconRotateClockwise.jpg ; and to rotate the image counterclockwise, click IconRotateCounterClockwise.jpg .


As with the direction arrow icons, you change the degree increment to achieve exact registration. The default degree increment is 1.0, but you can specify from 0.01 to 360 degrees. To change the degree increment, click IconSetPixelIncrement.jpg , the Set degree increment icon. The Change Degree Increment dialog box appears. Enter the degree increment in the Degree Increment box, and click Apply.

Registration: Manual 2D Series: Blended tab

Manual 2D Series window showing the Blended page

Show VOIs in blended window
Displays, on the Blended page, the VOIs that you delineated on the Dual page.
Blended tab
Displays the Blended page, which shows the image to be registered superimposed on the reference image. This page allows you to move and align the image to be registered with the reference image.
Dual tab
Displays the Dual page, which shows each image side by side, and allows you to delineate three or more landmarks on each image before you apply the Landmark-Least Squares algorithm or the Landmark-Thin Plate Spline algorithm to the images.
Alphablending slider
Adjusts the translucency of the alpha channels in each image using the alphablending technique. 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.
IconLookupTable.jpg Lookup table
Displays the Lookup Table window, which includes two tabs: Image A, the reference image, and Image B, the image to be registered.
IconCheckerboard.jpg Checkerboard A & B
Displays a checkerboard pattern on the images. You can use this pattern for assistance in aligning the images.
RegistrationManual2DSeries39.gif Magnify image 2.0x
Doubles the size of images, magnifying them to twice their current size. If an image is too large for the current window size, scroll bars appear, and you may need to manually adjust the size of the window.
To restore an image to its original size, use IconMinifyImage.jpg , the Magnify image 0.5x icon, as many times as you used this icon.
IconMinifyImage.jpg Magnify image 0.5x
Reduces the magnification level of images in half. To restore images to their original size, use the Magnify image 2.0x icon, as many times as you used this icon.
IconWindowRegionofImageB.jpg Window region of image B
Hides the reference image below a windowed mouse cursor; slide alphablending slider to the reference image
IconResetImagetoOriginalState.jpg Reset image to original state
Restores image to its original state. This icon deletes all points on the reference image and on the image to be registered. If the Apply button has already been selected, the Reset icon undoes all changes that occurred since the last time the Apply button was selected.
BtnApply.jpg Apply
Commits the changes that you made to the images, but it leaves the window open for you to make further changes if desired.
IconSetPixelIncrement.jpg Set pixel increment
Determines the number of pixels to use when any of the move image icons are used. When you click this icon, the Change Pixel Increment dialog box opens.
DialogboxChangePixelIncrement.jpg Although the default is 1.0, when the pixel increment is changed to another number, that number displays on the toolbar rather than 1.0. For example, if you changed the pixel increment to 550.0, this number would appear in the icon on the toolbar. You can use any pixel increment from 0.01 to 2048.00.
IconTranslateImage.jpg Translate image
Moves Image B, the image to be registered, in any direction you drag the image by the number of pixels indicated in the Set Pixel Increment icon.
IconMoveImageUp.jpg Move image up
Moves Image B, the image to be registered, up by the number of pixels indicated in the Set Pixel Increment icon.
IconMoveImageDown.jpg Move image down
Moves Image B, the image to be registered, down by the number of pixels indicated in the Set Pixel Increment icon.
IconMoveImageRight.jpg Move image right
Moves Image B, the image to be registered, right by the number of pixels indicated in the Set Pixel Increment icon.
IconMoveImageLeft.jpg Move image left
Moves Image B, the image to be registered, left by the number of pixels indicated in the Set Pixel Increment icon.
DialogboxChangeDegreeIncrement.jpg Set degree increment
Determines the degree to use when rotating images, rotating images clockwise, or rotating images counterclockwise. When you click this icon, the Change Degree Increment dialog box opens. Although the default degree increment is 1.0, when the degree increment is changed to another degree, that degree increment displays on the toolbar rather than 1.0. For example, if you changed the degree increment to 180.0, IconDegree180.jpg would appear on the toolbar. You can set the degree increment from 0.01 to 360.0.
IconRotateImage.jpg Rotate image
Allows you to select a center of rotation by clicking on the image with the mouse. It then allows you to then move the image above or below the center of rotation by dragging a line from the center of rotation.
IconRotateClockwise.jpg Rotate clockwise
Rotates the image to be registered clockwise by the number of degrees indicated as the degree increment. To restore the image to its original rotation, click IconReset.jpg , the Reset image to original state icon.
IconRotateCounterClockwise.jpg Rotate counterclockwise
Rotates the image to be registered counterclockwise by the number of degrees incited as the degree increment. To restore the image to its original rotation, click IconReset.jpg , the Reset image to original state icon.
Image area
Superimposes the image to be registered on the reference image and allows for the image to be registered to be moved, magnified, or rotated.

Manual 2D Series: Dual tab

Figure 6. Manual 2D Series window showing the Dual page

Show VOIs in blended window
Displays, on the Blended page, the VOIs that you delineated on the Dual page.
Blended tab
Displays the Blended page, which shows the image to be registered superimposed on the reference image. This page allows you to move and align the image to be registered with the reference image.
Dual tab
Displays the Dual page, which shows each image side by side, and allows you to delineate three or more landmarks on each image before you apply the Landmark-Least Squares algorithm or the Landmark-Thin Plate Spline algorithm to the images.
IconLookupTable.jpg Lookup Table
Displays the Lookup Table window, which includes two tabs: Image A, the reference image, and Image B, the image to be registered.
IconMagnifyReferenceImageto2.0x.jpg Magnify reference image 2.0x
Doubles the size of reference images, magnifying them to twice their current size. If an image is too large for the current window size, scroll bars appear, and you may need to manually adjust the size of the window.
To restore reference images to their original size, use IconMagnifyReferenceImageto0.5x.jpg , the Magnify reference image 0.5x icon, as many times as you used this icon.
IconMagnifyReferenceImageto0.5x.jpg Magnify reference image 0.5x
Reduces the magnification level of reference images in half. To restore reference images to their original size, use IconMagnifyReferenceImageto2.0x.jpg , the Magnify reference image 2.0x icon, as many times as you used this icon.
IconMagnifyAdjustedImage 2.0x.jpg Magnify adjusted image 2.0x
Doubles the size of adjusted images, magnifying them to twice their current size. If an image is too large for the current window size, scroll bars appear, and you may need to manually adjust the size of the window.
To restore adjusted images to their original size, use IconMagnifyAdjustedImage 0.5x.jpg , the Magnify reference image 0.5x icon, as many times as you used this icon.
IconMagnifyAdjustedImage 0.5x.jpg Magnify adjusted image 0.5x
Reduces the magnification level of adjusted images in half. To restore adjusted images to their original size, use IconMagnifyAdjustedImage 2.0x.jpg , the Magnify reference image 2.0x icon, as many times as you used this icon.
IconLeastSquaresAlignment.jpg Apply least squares alignment
Applies the Landmark-Least Squares algorithm to the image to be registered. After the algorithm is applied, if needed, you can apply the Landmark-Thin Plate Splines algorithm on the image, or you can manually adjust the alignment of the image on the Blended page.
IconThinPlateSplineAlignment.jpg Apply thin plate spline alignment
Applies the Landmark-Thin Plate Spline algorithm to the image to be registered. After this algorithm is applied, if needed, you can apply the Landmark-Least Squares algorithm on the image, or you can manually adjust the alignment of the image on the Blended page.
IconReset.jpg Reset image to original state
Restores the image to be registered to its original state. Restores image to its original state. This icon deletes all points on the reference image and on the image to be registered. If the Apply button has already been selected, the Reset icon undoes all changes that occurred since the last time the Apply button was selected.
IconReferenceSliceMarkers.jpg Reference slice markers
Adds a point to the reference image each time you click the left mouse button. Note that the points are sequentially labeled from 1 on in the order in which you created them. To remove points, return the cursor to its default mode by clicking IconReturntoDefaultMode.jpg , select the point to be deleted, and click IconDeleteSelectedReferenceSliceMarkers.jpg , Delete selected reference slice markers.
IconAdjustedSliceMarkers.jpg Adjusted slice markers
Adds a point to the adjusted image each time you click the left mouse button. Note that the points are sequentially labeled from 1 on in the order in which you created them. To remove points, return the cursor to its default mode by clicking IconReturntoDefaultMode.jpg , select the point to be deleted, and click IconDeleteSelectedAdjustedSliceMarkers.jpg , Delete selected adjusted slice markers.
IconDeleteSelectedReferenceSliceMarkers.jpg Delete selected reference slice markers
Removes the point that you selected in the reference image. To remove a point, first return the cursor to its default mode by clicking IconReturntoDefaultMode.jpg , select the point to be deleted, and click IconDeleteSelectedReferenceSliceMarkers.jpg , Delete selected reference slice markers.
IconDeleteSelectedAdjustedSliceMarkers.jpg Delete selected adjusted slice markers
Removes the point that you selected in the image to be registered. To remove a point, first return the cursor to its default mode by clicking IconReturntoDefaultMode.jpg , select the point to be deleted, and click IconDeleteSelectedAdjustedSliceMarkers.jpg , Delete selected adjusted slice markers.
IconReturntoDefaultMode.jpg Return to default mode
Returns the cursor to its default mode, which allows you to change from adding points to deleting points from the image.
BtnApply.jpg Apply
Commits the changes that you made to the images, but it leaves the window open for you to make further changes if desired.

Applying the Manual 2D Series algorithm on 2.5 images

To run this algorithm on 2.5D images, complete the following steps:
1 Open a single 2.5 image dataset. When you apply this algorithm, you select the slices in the dataset that you want to register.
2 Perform, as an option, any other image processing, except scaling, on the image dataset.
3 Select Algorithms > Registration > Manual 2D Series. The Manual 2D Series window for 2.5D images (see Figure 7]) opens.
Because you are registering slices of an image, and not separate images, all of the necessary icons and controls appear in a simple window that does not include tabbed pages. Note that there are two sliders at the top of the page:
Reference slice slider-Allows you to choose which slice to use as a reference image.
Adjusted slice slider-Allows you to choose which slice to use as an image to be registered.
The boxes to the right of each slider indicate which slice you are currently viewing.
All of the remaining icons and controls work in the same way that they do on the Manual 2D Series window for 2D images (refer to Figure 5 and Figure 6).

For 2.5D images, the algorithm's window does not include the Blended and Dual tabbed pages. Rather is incorporates some of the same interface controls that appear on the Blended and Dual pages, such as icons and the alphablending slider. Note that you can place landmarks on the image in this window.

References

For more information, refer to:

K.S. Arun, T.S. Huang, and S.D. Blostein, "Least-Squares Fitting of Two 3-D Point Sets" , IEEE Transactions on Pattern Analysis and Machine Intelligence, Vol. PAMI-9, No. 5, September, 1987, pp. 698-700.

David Eberly, "Thin Plate Splines" of Magic Software at http://www.magic-software.com. Also at the same site are the files: MgcInterp2DThinPlateSpline.h, MgcInterp2DThinPlateSpline.cpp, MgcInterp3DThinPlateSpline.h, MgcInterp3DThinPlateSpline.cpp Paper that explains warping from one x,y source to another x,y target set.

Fred L. BookStein, "Principal Warps: Thin-Plate Splines and the Decompositions of Deformations," IEEE Transactions on Pattern Analysis and Machine Intelligence, Vol. 11, No. 6, June 1989, pp. 567-585.


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