diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox index be92d7555b..864595e653 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox +++ b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox @@ -1,299 +1,303 @@ /** \page org_mitk_views_segmentation The Segmentation View \imageMacro{segmentation.svg,"Icon of the segmentation view",2.00} Some of the features described below are closed source additions to the open source toolkit MITK and are not available in every application. \tableofcontents \section org_mitk_views_segmentationUserManualOverview Overview Segmentation is the act of partitioning an image into subsets by either manual or automated delineation to create i.e. a distinction between foreground and background. The MITK segmentation plugin allows you to create segmentations of anatomical and pathological structures in medical images. The plugin consists of a number of views: In this documentation, the features and usage of the segmentation view will be described. For an introduction to the segmentation utilities and clipping plane views, please be referred to the respective documentation pages. \imageMacro{QmitkSegmentationPlugin_Overview.png,"Segmentation plugin overview", 16.00} \section org_mitk_views_segmentationPreferences Preferences The segmentation plugin offers a number of preferences which can be set via the MITK Workbench application preferences: \imageMacro{QmitkSegmentationPreferences.png,"Segmentation preferences", 10.00} \section org_mitk_views_segmentationUserManualTechnical Technical Issues The segmentation plugin makes a number of assumptions: \section org_mitk_views_segmentationUserManualImageSelection Data Selection & Creating New Segmentations To select a reference image for the segmentation, click on the Patient Image selection widget and choose a suitable image from the selection available in the data manager. By default the auto selection mode is enabled (see \ref org_mitk_views_segmentationPreferences).\n Once a patient image is selected, a new segmentation can be created on this reference image by clicking the New... button to the right of the Segmentation selection widget. An input field will appear which allows you to set the name and display color of the segmentation. Notice that the input field suggests names once you start typing and that it also suggests colors for known organ names. Once generated the segmentation will be added with "binary mask" icon to the data manager as sub-node of the reference image. This item is automatically selected for you, allowing you to start editing the new segmentation right away. \subsection org_mitk_views_segmentationUserManualManualKringeling2 Selecting Segmentations for Editing Alternatively to creating a new segmentation, an existing one can be edited as well. As you might have segmented multiple structures within a single image, the application needs to know which of them to use for editing. For that you click the segmentation selection widget and a selection field will open, containing all suitable segmentations for the parent dataset available in the data manager. \section org_mitk_views_segmentationUserManualToolOverview Segmentation Tool Overview MITK offers a comprehensive set of slice-based 2D and (semi-)automated 3D segmentation tools. The manual 2D tools require some user interaction and can only be applied to a single image slice whereas the 3D tools operate on the whole image. The 3D tools usually only require a small amount of user interaction, i.e. placing seed points or setting/adjusting parameters. You can switch between the different toolsets by selecting the 2D or 3D tab in the segmentation view. \imageMacro{QmitkSegmentation_ToolOverview.png,"An overview of the existing 2D and 3D tools in MITK.",5.50} \section org_mitk_views_segmentationUserManualManualKringeling 2D Segmentation Tools With 2D manual contouring you define which voxels are part of the segmentation and which ones are not. This allows you to create segmentations of any structures of interest in an image. You can also use manual contouring to correct segmentations that result from sub-optimal automatic methods. The drawback of manual contouring is that you might need to define contours on many 2D slices. However, this is mitigated by the interpolation feature, which will make suggestions for a segmentation. \subsection org_mitk_views_segmentationUserManualManualKringeling3 Selecting Editing Tools To start using one of the editing tools, click its button from the displayed toolbox. The selected editing tool will be active and its corresponding button will stay pressed until you click the button again. Selecting a different tool also deactivates the previous one.\n If you have to delineate a lot of images, shortcuts to switch between tools becomes convenient. For that, just hit the first letter of each tool to activate it (A for Add, S for Subtract, etc.). \subsection org_mitk_views_segmentationUserManualManualKringeling4 Using Editing Tools All of the editing tools work by the same principle: you use the mouse (left button) to click anywhere in a 2D window (any of the orientations axial, sagittal, or coronal), move the mouse while holding the mouse button and release to finish the editing action. Multi-step undo and redo is fully supported by all editing tools. Use the application-wide undo button in the toolbar to revert erroneous %actions. Remark: If you are familiar with the MITK Workbench, you know that clicking and moving the mouse in any of the 2D render windows will move around the crosshair that defines what part of the image is displayed. This behavior is disabled whilst any of the manual segmentation tools are active- otherwise you might have a hard time concentrating on the contour you are drawing. \subsection org_mitk_views_segmentationUserManualAddSubtractTools Add and Subtract Tools \imageMacro{QmitkSegmentation_IMGIconAddSubtract.png,"Add and Subtract Tools",7.70} Use the left mouse button to draw a closed contour. When releasing the mouse button, the contour will be added (Add tool) to or removed (Subtract tool) from the current segmentation. Adding and subtracting voxels can be iteratively repeated for the same segmentation. Holding CTRL / CMD while drawing will invert the current tool's behavior (i.e. instead of adding voxels, they will be subtracted). \subsection org_mitk_views_segmentationUserManualPaintWipeTools Paint and Wipe Tools \imageMacro{QmitkSegmentation_IMGIconPaintWipe.png,"Paint and Wipe Tools",7.68} Use the Size slider to change the radius of the round paintbrush tool. Move the mouse in any 2D window and press the left button to draw or erase pixels. Holding CTRL / CMD while drawing will invert the current tool's behavior (i.e. instead of painting voxels, they will be wiped). \subsection org_mitk_views_segmentationUserManualRegionGrowingTool Region Growing Tool \imageMacro{QmitkSegmentation_IMGIconRegionGrowing.png,"Region Growing Tool",3.81} Click at one point in a 2D slice widget to add an image region to the segmentation with the region growing tool. Region Growing selects all pixels around the mouse cursor that have a similar gray value as the pixel below the mouse cursor. This enables you to quickly create segmentations of structures that have a good contrast to surrounding tissue. -Moving up the cursor while holding the left mouse button widens the range for the included grey values; moving it down narrows it. Moving the mouse left and right will shift the range. +The tool operates based on the current level window, so changing the level window to optimize the contrast for the ROI is encouraged. +Moving the mouse up/down is different from left/right: Moving up the cursor while holding the left mouse button widens the range for the included grey values; moving it down narrows it. Moving the mouse left and right will shift the range. The tool will select more or less pixels, corresponding to the changing gray value range. + + + \if THISISNOTIMPLEMENTEDATTHEMOMENT A common issue with region growing is the so called "leakage" which happens when the structure of interest is connected to other pixels, of similar gray values, through a narrow "bridge" at the border of the structure. The Region Growing tool comes with a "leakage detection/removal" feature. If leakage happens, you can left-click into the leakage region and the tool will try to automatically remove this region (see illustration below). \imageMacro{QmitkSegmentation_IMGLeakage.png,"Leakage correction feature of the Region Growing tool",11.28} \endif \subsection org_mitk_views_segmentationUserManualCorrectionTool Correction Tool
\imageMacro{QmitkSegmentation_IMGIconCorrection.png,"Correction Tool",3.77} You do not have to draw a closed contour to use the Correction tool and do not need to switch between the Add and Substract tool to perform small corrective changes. The following figure shows the usage of this tool: \imageMacro{QmitkSegmentation_IMGCorrectionActions.png,"Usage of the Correction tool.",13.50}
\subsection org_mitk_views_segmentationUserManualFillTool Fill Tool \imageMacro{QmitkSegmentation_IMGIconFill.png,"Fill Tool",3.81} Left-click inside a segmentation with holes to completely fill all holes. Left-click inside a hole to fill only this specific hole. \subsection org_mitk_views_segmentationUserManualEraseTool Erase Tool \imageMacro{QmitkSegmentation_IMGIconErase.png,"Erase Tool",3.79} This tool removes a connected part of pixels that form a segmentation. You may use it to remove single segmentations (left-click on specific segmentation) or to clear a whole slice at once (left-click outside a segmentation). \subsection org_mitk_views_segmentationUserManualLiveWireTool Live Wire Tool \imageMacro{QmitkSegmentation_IMGIconLiveWire.png,"Live Wire Tool",3.01} The Live Wire Tool acts as a magnetic lasso with a contour snapping to edges of objects. \imageMacro{QmitkSegmentation_IMGLiveWireUsage.PNG,"Steps for using the Live Wire Tool",16.00} The contour will be transferred to its binary image representation by deactivating the tool. \subsection org_mitk_views_segmentationUserManual2DFastMarchingTool 2D Fast Marching Tool \imageMacro{QmitkSegmentation_IMG2DFastMarchingUsage.png,"2D Fast Marching Tool",3.01} Provides a fast marching based 2D interaction segmentation tool. You start with setting seed points in an image slice. Via several sliders you can adapt parameters and see the fast marching result instantly. \subsection org_mitk_views_segmentationUserManualManualKringeling5 2D and 3D Interpolation Creating segmentations using 2D manual contouring for large image volumes may be very time-consuming, because structures of interest may cover a large range of slices. The segmentation view offers two helpful features to mitigate this drawback: The 2D Interpolation creates suggestions for a segmentation whenever you have a slice that \imageMacro{QmitkSegmentation_2DInterpolation.png,"2D Interpolation Usage",3.01} Interpolated suggestions are displayed as outlines, until you confirm them as part of the segmentation. To confirm single slices, click the Confirm for single slice button below the toolbox. You may also review the interpolations visually and then accept all of them at once by selecting Confirm for all slices. The 3D interpolation creates suggestions for 3D segmentations. That means if you start contouring, from the second contour onwards, the surface of the segmented area will be interpolated based on the given contour information. The interpolation works with all available manual tools. Please note that this is currently a pure mathematical interpolation, i.e. image intensity information is not taken into account. With each further contour the interpolation result will be improved, but the more contours you provide the longer the recalculation will take. To achieve an optimal interpolation result and in this way a most accurate segmentation you should try to describe the surface with sparse contours by segmenting in arbitrary oriented planes. The 3D interpolation is not meant to be used for parallel slice-wise segmentation, but rather segmentations in i.e. the axial, coronal and sagittal plane. \imageMacro{QmitkSegmentation_3DInterpolationWrongRight.png,"3D Interpolation Usage",16.00} You can accept the interpolation result by clicking the Confirm-button below the tool buttons. In this case the 3D interpolation will be deactivated automatically so that the result can be post-processed without any interpolation running in the background. Additional to the surface, black contours are shown in the 3D render window, which mark all the drawn contours used for the interpolation. You can navigate between the drawn contours by clicking on the corresponding position nodes in the data manager which are stored as sub-nodes of the selected segmentation. If you do not want to see these nodes just uncheck the Show Position Nodes checkbox and these nodes will be hidden. If you want to delete a drawn contour we recommend to use the Erase-Tool since Redo/Undo is not yet working for 3D interpolation. The current state of the 3D interpolation can be saved across application restart. For that, just click on save project during the interpolation is active. After restarting the application and load your project you can click on "Reinit Interpolation" within the 3D interpolation GUI area. \section org_mitk_views_segmentationUserManual3DSegmentationTools 3D Segmentation Tools The 3D tools operate on the whole image and require usually a small amount of interaction like placing seed-points or specifying certain parameters. All 3D tools provide an immediate segmentation feedback, which is displayed as a transparent green overlay. For accepting a preview you have to press the Confirm button of the selected tool. The following 3D tools are available: \subsection org_mitk_views_segmentationUserManual3DThresholdTool 3D Threshold Tool The thresholding tool simply applies a 3D threshold to the patient image. All pixels with values equal or above the selected threshold are labeled as part of the segmentation. You can change the threshold by either moving the slider of setting a certain value in the spinbox. \imageMacro{QmitkSegmentation_3DThresholdTool.png,"3D Threshold tool",10.00} \subsection org_mitk_views_segmentationUserManual3DULTool 3D Upper/Lower Threshold Tool The Upper/Lower Thresholding tool works similar to the simple 3D threshold tool but allows you to define an upper and lower threshold. All pixels with values within this threshold interval will be labeled as part of the segmentation. \imageMacro{QmitkSegmentation_3DULThresholdTool.png,"3D Upper/Lower Threshold tool",10.00} \subsection org_mitk_views_segmentationUserManual3DOtsuTool 3D Otsu Tool The 3D Otsu tool provides a more sophisticated thresholding algorithm. It allows you to define a number of regions. Based on the image histogram the pixels will then be divided into different regions. The more regions you define the longer the calculation will take. You can select afterwards which of these regions you want to confirm as segmentation. \imageMacro{QmitkSegmentation_3DOtsuTool.png,"3D Otsu tool",10.00} \subsection org_mitk_views_segmentationUserManual3DFMTool 3D Fast Marching Tool The 3D Fast Marching tool works similar to the 2D pendant but on the whole image. Depending on your image size the calculation might take some time. You can interactively set the parameters of the algorithm via the GUI. The resulting segmentation will be automatically updated. \imageMacro{QmitkSegmentation_3DFMTool.png,"3D Fast Marching tool",10.00} \subsection org_mitk_views_segmentationUserManual3DRGTool 3D Region Growing Tool The 3D Region Growing tool works similar to the 2D pendant. At the beginning you have to place a seedpoint and define a threshold interval. If you press Run Segmentation a preview is calculated. By moving the Adapt region growing slider you can interactively adapt the segmentation result. \imageMacro{QmitkSegmentation_3DRGTool.png,"3D Region Growing tool",10.00} \subsection org_mitk_views_segmentationUserManual3DWatershedTool 3D Watershed Tool This tool provides a watershed based segmentation algorithm. For further information please be referred to the relevant literature, i.e. \imageMacro{QmitkSegmentation_3DWatershedTool.png,"3D Watershed tool",10.00} \subsection org_mitk_views_segmentationUserManualPickingTool Picking Tool The Picking tool allows you to select islands within your segmentation. This is especially useful if e.g. a thresholding provided you with several areas within your image but you are just interested in one special region. \imageMacro{QmitkSegmentation_PickingTool.png,"Picking tool",10.00} \section org_mitk_views_segmentationUserManualPostprocessing Additional things you can do with segmentations Segmentations are never an end in themselves. Consequently, the segmentation view adds a couple of "post-processing" actions, accessible through the context-menu of the data manager. \imageMacro{QmitkSegmentation_IMGDataManagerContextMenu.png,"Context menu items for segmentations.",10.58} \section org_mitk_views_segmentationof3DTImages Segmentation of 3D+t images For segmentation of 3D+t images, some tools give you the option to choose between creating dynamic and static masks. In general, segmentation is applied on the time frame that is selected when execution is performed. If you alter the time frame, the segmentation preview is adapted. \section org_mitk_views_segmentationUserManualTechnicalDetail Technical Information for Developers For technical specifications see \subpage QmitkSegmentationTechnicalPage and for information on the extensions of the tools system \subpage toolextensions . */