diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/QmitkSegmentationTechnical.dox b/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/QmitkSegmentationTechnical.dox deleted file mode 100644 index b8992e8a55..0000000000 --- a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/QmitkSegmentationTechnical.dox +++ /dev/null @@ -1,101 +0,0 @@ -/** - -\page QmitkSegmentationTechnicalPage Technical design of QmitkSegmentation - -\li \ref QmitkSegmentationTechnicalPage2 -\li \ref QmitkSegmentationTechnicalPage3 -\li \ref QmitkSegmentationTechnicalPage4 - -\section QmitkSegmentationTechnicalPage2 Introduction - -QmitkSegmentation was designed for the liver resection planning -project "ReLiver". -The goal was a stable, well-documented, extensible, and testable -re-implementation of a functionality called "ERIS", which was used for manual -segmentation in 2D slices of 3D or 3D+t images. -Re-implementation was chosen because it seemed to be easier to write -documentation and tests for newly developed code. In addition, the old code had -some design weaknesses (e.g. a monolithic class), which would be hard to -maintain in the future. - -By now Segmentation is a well tested and easily extensible vehicle for all kinds of interactive -segmentation applications. A separate page describes how you can extend Segmentation with new -tools in a shared object (DLL): \ref toolextensions. - -\section QmitkSegmentationTechnicalPage3 Overview of tasks - -We identified the following major tasks: - -
    -
  1. Management of images: what is the original patient image, what -images are the active segmentations? -
  2. Management of drawing tools: there is a set of drawing tools, one at -a time is active, that is, someone has to decide which tool will receive mouse -(and other) events. -
  3. Drawing tools: each tool can modify a segmentation in reaction to -user interaction. To do so, the tools have to know about the relevant images. -
  4. Slice manipulation: drawing tools need to have means to extract a -single slice from an image volume and to write a single slice back into an image -volume. -
  5. Interpolation of unsegmented slices: some class has to keep track of -all the segmentations in a volume and generate suggestions for missing slices. -This should be possible in all three orthogonal slice direction. -
  6. Undo: Slice manipulations should be undoable, no matter whether a -tool or the interpolation mechanism changed something. -
  7. GUI: Integration of everything. -
- - -\section QmitkSegmentationTechnicalPage4 Classes involved - -The above blocks correspond to a number of classes. Here is an overview of all -related classes with their responsibilities and relations: - -\imageMacro{"interactive_segmentation_classes.png","html",12} - -
    -
  1. Management of images: mitk::ToolManager has a set of reference -data (original images) and a second set of working data (segmentations). -mitk::Tool objects know a ToolManager and can ask the manager for the currently -relevant images. There are two GUI elements that enable -the user to modify the set of reference and working images (QmitkToolReferenceDataSelectionBox and QmitkToolWorkingDataSelectionBox). GUI and non-GUI -classes are coupled by itk::Events (non-GUI to GUI) and direct method calls (GUI -to non-GUI). -
  2. Management of drawing tools: As a second task, ToolManager manages all available tools and makes sure that one at a time is able to receive MITK events. -The GUI for selecting tools is implemented in QmitkToolSelectionBox. -
  3. Drawing tools: Drawing tools all inherit from mitk::Tool, which is a -mitk::StateMachine. There is a number of derivations from Tool, each offering -some helper methods for specific sub-classes, like manipulation of 2D slices. -Tools are instantiated through the itk::ObjectFactory, which means that there is -also one factory for each tool (e.g. mitk::AddContourToolFactory). For the GUI representation, each tool has an -identification, consisting of a name and an icon (XPM). The actual drawing -methods are mainly implemented in mitk::SegTool2D (helper methods) and its -sub-classes for region growing, freehand drawing, etc. -
  4. Slice manipulation: There are two filters for manipulation of slices -inside a 3D image volume. mitk::ExtractImageFilter retrieves a single 2D slice -from a 3D volume. mitk::OverwriteSliceImageFilter replaces a slice inside a 3D -volume with a second slice which is a parameter to the filter. These classes are -used extensively by most of the tools to fulfill their task. -mitk::OverwriteSliceImageFilter cooperates with the interpolation classes to -inform them of single slice modifications. -
  5. Interpolation of unsegmented slices: There are two classes involved -in interpolation: mitk::SegmentationInterpolationController knows a mitk::Image (the -segmentation) and scans its contents for slices with non-zero pixels. It keeps -track of changes in the image and is always able to tell, which neighbors of a -slice (in the three orthogonal slice directions) contain segmentations. The -class also performs this interpolation for single slices on demand. -Again, we have a second class responsible for the GUI: -QmitkSlicesInterpolator enables/disables interpolation and offers to -accept interpolations for one or all slices. -
  6. Undo: Undo functionality is implemented in mitk::OverwriteSliceImageFilter, -since this is the central place where all image modifications are made. The filter stores a binary difference image -to the undo stack as a mitk::ApplyDiffImageOperation. When the user requests undo, this ApplyDiffImageOperation -will be executed by a singleton class DiffImageApplier. The operation itself observes the image, which it refers to, -for itk::DeleteEvent, so no undo operation will be executed on/for images that have already been destroyed. -
  7. GUI: The top-level GUI is the functionality -QmitkSegmentation, which is very thin in comparison to ERIS. There are -separate widgets for image and tool selection, for interpolation. Additionaly, -there are some methods to create, delete, crop, load and save segmentations. -
- -**/ diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/ToolExtensionsGeneralOverview.dox b/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/ToolExtensionsGeneralOverview.dox deleted file mode 100644 index 6df1762137..0000000000 --- a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/ToolExtensionsGeneralOverview.dox +++ /dev/null @@ -1,181 +0,0 @@ -/** - -\page toolextensions How to extend the Segmentation view with external tools - - - -\section ToolExtensionsGeneralOverview2 Introduction - -The application for manual segmentation in MITK (Segmentation view) comes -with a tool class framework that is extensible with new tools (description at -\ref QmitkSegmentationTechnicalPage). The usual way -to create new tools (since it is mostly used inside DKFZ) is to just add new -files to the MITK source code tree. However, this requires to be familiar with -the MITK build system and turnaround time during development might be long -(recompiling parts of MITK again and again). - -For external users who just want to use -MITK as a library and application, there is a way to create new segmentation -tools in an MITK external project, which will compile the new tools into a -shared object (DLL). Such shared objects can be loaded via the ITK object factory -and its autoload feature on application startup. This document describes -how to build such external extensions. - -Example files can be found in the MITK source code in the directory -${MITK_SOURCE_DIR}/QApplications/ToolExtensionsExample/. - -\section ToolExtensionsGeneralOverview3 What might be part of an extension - -The extension concept assumes that you want to create one or several new -interactive segmentation tools for Segmentation or another MITK -functionality that uses the tools infrastructure. In the result you -will create a shared object (DLL), which contains several tools and their GUI -counterparts, plus optional code that your extension requires. The following -sections shortly describe each of these parts. - -\subsection ToolExtensionsGeneralOverview31 Tool classes - -A tool is basically any subclass of mitk::Tool. Tools are created at runtime -through the ITK object factory (so they inherit from itk::Object). Tools -should handle the interaction part of a segmentation method, i.e. create -seed points, draw contours, etc., in order to parameterize segmentation algorithms. -Simple algorithms can even be part of a tool. A tools is identified by icon (XPM format), -name (short string) and optionally a group name (e.g. the group name for Segmentation -is "default"). - -There is a naming convention: you should put a tool called \c mitk::ExternalTool into -files called \c mitkExternalTool.h and \c mitkExternalTool.cpp. This is \e required if -you use the convenience macros described below, because there need to be ITK factories, -which names are directly derived from the file names of the tools. For the example of mitk::ExternalTool -there would be a factory called \c mitk::ExternalToolFactory in a file named \c mitkExternalToolFactory.cpp. - -\subsection ToolExtensionsGeneralOverview32 GUI classes for tools - -Tools are non-graphical classes that only implement interactions in renderwindows. However, -some tools will need a means to allow the user to set some parameters -- a graphical user interface, GUI. -In the Qt3 case, tool GUIs inherit from QmitkToolGUI, which is a mixture of QWidget and itk::Object. -Tool GUIs are also created through the ITK object factory. - -Tools inform their GUIs about state changes by messages. Tool GUIs communicate with their associated tools -via direct method calls (they know their tools). See mitk::BinaryThresholdTool for examples. - -Again a naming convention: if the convenience macros for tool extension shared objects are used, -you have to put a tool GUI called \c QmitkExternalToolGUI into a files named \c QmitkExternalToolGUI.cpp -and \c QmitkExternalToolGUI.h. The convenience macro will create a factory called \c QmitkExternalToolGUIFactory -into a file named \c QmitkExternalToolGUIFactory.cpp. - -\subsection ToolExtensionsGeneralOverview33 Additional files - -If you are writing tools MITK externally, these tools might depend on additional files, e.g. -segmentation algorithms. These can also be compiled into a tool extension shared object. - -\section ToolExtensionsGeneralOverview4 Writing a CMake file for a tool extension - -Summing up the last section, an example tool extension could comprise the following files: -\verbatim -mitkExternalTool.h \ -mitkExternalTool.xpm >--- implementing mitk::ExternalTool (header, icon, implementation) -mitkExternalTool.cpp / - -QmitkExternalToolGUI.h ,-- implementing a GUI for mitk::ExternalTool -QmitkExternalToolGUI.cpp / - -externalalgorithm.h \ -externalalgorithm.cpp \ -externalalgorithmsolver.h >-- a couple of files (not related to MITK tools) -externalalgorithmsolver.cpp / -\endverbatim - -This should all be compiled into one shared object. Just like ITK, VTK and MITK we -will use CMake for this purpose (I assume you either know or are willing to learn about -www.cmake.org) -A CMake file for the above example would look like this: - -\code -project( ExternalTool ) - -find_package(ITK) -find_package(MITK) -find_package(Qt3) - -add_definitions(${QT_DEFINITIONS}) - -set( TOOL_QT3GUI_FILES - QmitkExternalToolGUI.cpp - ) - -set( TOOL_FILES - mitkExternalTool.cpp - ) - -set( TOOL_ADDITIONAL_CPPS - externalalgorithm.cpp - externalalgorithmsolver.cpp - ) - -set( TOOL_ADDITIONAL_MOC_H -) - -MITK_GENERATE_TOOLS_LIBRARY(mitkExternalTools) -\endcode - -Basically, you only have to change the definitions of \c TOOL_FILES and, optionally, -\c TOOL_QT3GUI_FILES, \c TOOL_ADDITIONAL_CPPS and \c TOOL_ADDITIONAL_MOC_H. -For all .cpp files in \c TOOL_FILES and \c TOOL_QT3GUI_FILES there will be factories -created assuming the naming conventions described in the sections above. -Files listed in \c TOOL_ADDITIONAL_CPPS will just be compiled. Files listed in -\c TOOL_ADDITIONAL_MOC_H will be run through Qts meta object compiler \c moc -- -this is neccessary for all objects that have the Q_OBJECT macro in their declaration. -\c moc will create new files that will also be compiled into the library. - -\section ToolExtensionsGeneralOverview5 Compiling the extension - -For compiling a tool extension, you will need a compiled version of MITK. We will -assume MITK was compiled into /home/user/mitk/debug. You need to build MITK with -BUILD_SHARED_CORE turned on! - -You build the tool extension just like any other CMake based project: -\li know where your source code is (e.g. /home/user/mitk/tool-extension-src) -\li change into the directory, where you want to compile the shared object (e.g. /home/user/mitk/tool-extension-debug) -\li invoke cmake: ccmake /home/user/mitk/tool-extension-src -\li configure (press c or the "configure" button) -\li set the ITK_DIR variable to the directory, where you compiled ITK -\li set the MITK_DIR variable to the directory, where you compiled MITK: /home/user/mitk/debug -\li configure (press "c" or the "configure" button) -\li generate (press "g" or the "generate" button) - -This should do it and leave you with a or project file or Makefile that you can compile (using make or VisualStudio). - -\section ToolExtensionsGeneralOverview6 Configuring ITK autoload - -If the compile succeeds, you will get a library mitkExternalTools.dll or libmitkExternalTools.so. -This library exports a symbol \c itkLoad which is expected by the ITK object factory. - -On application startup the ITK object factory will search a list of directories from -the environment variable \c ITK_AUTOLOAD_PATH. Set this environment variable to your -binary directory (/home/user/mitk/tool-extension-debug). - -The ITK object factory will load all shared objects that it finds in the specified directories -and will test if they contain a symbol (function pointer) \c itkLoad, which is expected -to return a pointer to a itk::ObjectFactoryBase instance. If such a symbol is found, the -returned factory will be registered with the ITK object factory. - -If you successfully followed all the steps above, MITK will find your mitk::ExternalTool on -application startup, when the ITK object factory is asked to create all known instances of -mitk::Tool. Furthermore, if your mitk::ExternalTool claims to be part of the "default" group, -there will be a new icon in Segmentation, which activates your tool. - -Have fun! (And Windows users: welcome to the world of DLLs) - -**/ diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/interactive_segmentation_classes.png b/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/interactive_segmentation_classes.png deleted file mode 100644 index 9a9a4382f7..0000000000 Binary files a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/interactive_segmentation_classes.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/interactive_segmentation_classes.xcf b/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/interactive_segmentation_classes.xcf deleted file mode 100644 index 6e37987eb4..0000000000 Binary files a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/interactive_segmentation_classes.xcf and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_gui_qt_multilabelsegmentation.dox b/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_gui_qt_multilabelsegmentation.dox index aad48c7a28..77069cfa4b 100644 --- a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_gui_qt_multilabelsegmentation.dox +++ b/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_gui_qt_multilabelsegmentation.dox @@ -1,396 +1,114 @@ /** \page org_mitk_views_multilabelsegmentation The Multilabel Segmentation View \imageMacro{"multilabelsegmentation.png", "html", 12} -Some of the features described below are closed source additions to the open source toolkit MITK and are not -available in every application. - -Available sections: - - - \ref org_mitk_gui_qt_segmentationUserManualOverview - - \ref org_mitk_gui_qt_segmentationUserManualTechnical - - \ref org_mitk_gui_qt_segmentationUserManualCreateOpenSaveImportAdd - - \ref org_mitk_gui_qt_segmentationUserManualLabelTable - - \ref org_mitk_gui_qt_segmentationUserManualLabelCreation - - \ref org_mitk_gui_qt_segmentationUserManualLayerCreation - - \ref org_mitk_gui_qt_segmentationUserManualLabelSearch - - \ref org_mitk_gui_qt_segmentationUserManualLabelEditing - - \ref org_mitk_gui_qt_segmentationUserManualContouring - - \ref org_mitk_gui_qt_segmentationUserManualInterpolation - - \ref org_mitk_gui_qt_segmentationUserManualOrganSegmentation - - \ref org_mitk_gui_qt_segmentationUserManualOrganSegmentation1 - - \ref org_mitk_gui_qt_segmentationUserManualOrganSegmentation2 - - \ref org_mitk_gui_qt_segmentationUserManualOrganSegmentation99 - - \ref org_mitk_gui_qt_segmentationUserManualLesionSegmentation - - \ref org_mitk_gui_qt_segmentationUserManualOperationsOnLabels - - \ref org_mitk_gui_qt_segmentationUserManualOperationsOnSingleSelection - - \ref org_mitk_gui_qt_segmentationUserManualOperationsOnMultipleSelection - - \ref org_mitk_gui_qt_segmentationUserManualSegmentationUtilities - - \ref org_mitk_gui_qt_segmentationUserManualTechnicalDetail - -\section org_mitk_gui_qt_segmentationUserManualOverview Overview - -The Segmentation Perspective allows to create segmentations of structures of interest in biomedical and biological -images. Examples of such structures are an organ, a vessel or a lesion in a CT or MR image, or a cell or organelle in microscopy -images. The perspective groups a number of tools which can be used for: - - -\imageMacro{"org_mitk_gui_qt_segmentationIMGapplication.png", "Segmentation perspective consisting of the Data Manager view, the -Segmentation view and the Segmentation Utilities view.", 12} - -If you wonder what segmentations are good for, we shortly revisit the concept of a segmentation here. -A CT or MR image is made up of volume of physical measurements (volume elements are called voxels). -In CT images, for example, the gray value of each voxel corresponds to the mass absorption coefficient -for X-rays in this voxel, which is similar in many %parts of the human body. -The gray value does not contain any further information, so the computer does not know whether a given -voxel is part of the body or the background, nor can it tell a brain from a liver. -However, the distinction between voxels belonging to an object and a background structure is required when: - - -This distinction between voxels inside and object and background is called segmentation. -Since many objects might be segmented on an image, each segmentation is assigned a different label. A label -has a name, a color, and a number of properties that we will describe later. -The current implementation of the Segmentation perspective uses a voxel-based approach for segmentations, i.e. each voxel -of an image must be completely assigned to either a label or background. In a future version of the toolkit we will also enable -the generation of segmentations based on contours. In this way, the user will be able to better define the borders of the -segmented objects by taking advantage of his/her medical knowledge. Segmentations based on contours are not restricted to -the voxel size of the medical image and can be arbitrarily positioned. - -The remainder of this document will summarize the features of the Segmentation perspective and how they are used. +Please reference \ref org_mitk_views_segmentation for the description of the general segmentation tools. -\subsection org_mitk_gui_qt_segmentationUserManualTechnical Technical Issues +\tableofcontents -The Segmentation Perspective makes a number of assumptions. To know what this view can be used for, it will help you to know that: - - -\section org_mitk_gui_qt_segmentationUserManualCreateOpenSaveImportAdd Start Segmenting +\section org_mitk_views_multilabelsegmentationUserManualCreateOpenSaveImportAdd Start Segmenting To start using the Segmentation Perspective you will have to either create a new segmentation session or load an existing one from disk. The Segmentation toolbar collects buttons for the these actions: -\imageMacro{"org_mitk_gui_qt_segmentationIMGtoolbar.png", "Segmentation toolbar", 12} +\imageMacro{"org_mitk_views_multilabelsegmentationIMGtoolbar.png", "Segmentation toolbar", 12} -\section org_mitk_gui_qt_segmentationUserManualLabelTable The Label Table +\section org_mitk_views_multilabelsegmentationUserManualLabelTable The Label Table The following label properties are readily available to modify: The Label Table is shown below: -\imageMacro{org_mitk_gui_qt_segmentationIMGlabeltable.png", "The Label Table showing all the labels in the current segmentation session", 12} +\imageMacro{"org_mitk_views_multilabelsegmentationIMGlabeltable.png", "The Label Table showing all the labels in the current segmentation session", 12} -\section org_mitk_gui_qt_segmentationUserManualLabelCreation Creating a New Label +\section org_mitk_views_multilabelsegmentationUserManualLabelCreation Creating a New Label Click the "New Label" button to add a new label. A dialog will show-up to enter the name and color. Preset organ names and corresponding colors are offered while you type in, but you can set any name. The new name if not known will be automatically remembered and made available the next time you create a new label. In the current implementation of the plugin, the maximum number of labels is restricted to 255. If you need more, you will have to create a new segmentation session. -\section org_mitk_gui_qt_segmentationUserManualLayerCreation Creating a New Layer +\section org_mitk_views_multilabelsegmentationUserManualLayerCreation Creating a New Layer A layer is a set of labels that occupy a non-overlapping anatomical space. The best way to describe them is by a real use case. Imagine you are working on a radiotherpay planning application. In the first layer of your segmentation session you would like to trace the contours of the liver and neighboring organs. You can accomodate all these segmentations in separate labels because they all occupy different anamical regions and do not overlap. Now say you would like to segment the arteries and veins inside the liver. If you don´t trace them in a different layer, you will overwrite the previous ones. You may also need a third layer for segmenting the different irrigation territories in the liver and a fourth layer to contain the lession you would like to treat. The next figure illustrates the Layer Manager . The buttons in it contained serve for adding a new layer, selecting the previous and the next one. The active layer is shown together with the buttons. -\imageMacro{"org_mitk_gui_qt_segmentationIMGlayerManager.png", "Correction Tool",12} +\imageMacro{"org_mitk_views_multilabelsegmentationIMGlayerManager.png", "Correction Tool",12} -\section org_mitk_gui_qt_segmentationUserManualLabelSearch Searching a Label +\section org_mitk_views_multilabelsegmentationUserManualLabelSearch Searching a Label It may happen that many labels (e.g. > 200) are present in a segmentation session and therefore manual searching is time consuming. The Label Search edit box allows for quickly finding the label you want. Just start writing its name and and you will get assitance for completing its name. If the label you were searching is found, press enter and it will became the active one. -\imageMacro{"org_mitk_gui_qt_segmentationIMGsearchlabel.png", "Label search", 12} +\imageMacro{"org_mitk_views_multilabelsegmentationIMGsearchlabel.png", "Label search", 12} -\section org_mitk_gui_qt_segmentationUserManualLabelEditing Label Editing +\section org_mitk_views_multilabelsegmentationUserManualLabelEditing Label Editing First of all, you have to select the active label by clicking on the corresponding row in the Label Table. Only one label can be active at the time. Then you can select an editing tool in the toolbox. -The selected editing tool will be active and its corresponding button will stay pressed until you click the same button again. -Selecting a different tool also deactivates the previous one. If you are familiar with the MITK Workbench, you know that -clicking and moving the mouse in any of the 2D windows will move around the crosshair that defines the position in -the image you are standing on. Depending on the tool that you activate, this behavior may be disabled during segmenting --- otherwise you might have a hard time concentrating on the contour you are drawing --. - -If you have to delineate a lot of images, you should try using shortcuts to switch tools. Just hit the first letter of each -tool to activate it (e.g. "A" for Add, "S" for Subtract, etc.). If you hover the cursor on a tool button you will get a tip -message reminding you this. - -\subsection org_mitk_gui_qt_segmentationUserManualManualEditingTools Manual 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 frontal), move the mouse while holding the mouse button and -release to finish the editing action. - -At any time you can undo or redo your past actions with corresponding buttons in the application\'s toolbar. - -\subsection org_mitk_gui_qt_segmentationUserManualContouring Manual Contouring - -The "Add" and "Subtract" tools allow for freely tracing a contour around an organ or structure in an image. -You might also use manual contouring to further enhance or correct a segmentation resulting from sub-optimal automatic methods. -The drawback of manual contouring is that you might need to define contours on many 2D slices to segment the whole structure. -However, this is moderated by the interpolation tools, which are described later. - -\imageMacro{"org_mitk_gui_qt_segmentationIMGiconAddSubtract.png", "Add and Subtract Tools",12} - -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 from (Subtract tool) the current segmentation. -Hold down the CTRL / CMD key to invert the operation (this will switch tools temporarily to allow for quick corrections). - -\imageMacro{"org_mitk_gui_qt_segmentationIMGiconPaintWipe.png", "Paint and Wipe Tools", 12cm} - -Use the slider below the toolbox to change the radius of the paintbrush tool. Move the mouse -in any 2D window and press the left button to draw or erase the active label. -As the Add/Subtract tools, holding CTRL/CMD while drawing will invert the current tool's behavior. - -\imageMacro{"org_mitk_gui_qt_segmentationIMGiconRegionGrowing.png", "Region Growing Tool", 12} - -Click with the left button at one point in a 2D window and move up or down while keeping it pressed. This action -will make your segmentation grow (up) or shrink (down). When working on an image with a high range of grey values, -the selection range can be influenced more strongly by moving the cursor at higher velocity. The region growing algorithm -tool selects all pixels around the mouse cursor that have a similar gray value as the pixel below the first clicked position. -This enables you to quickly create segmentations of structures that have a good contrast to surrounding tissue, e.g. the lungs. - -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{"org_mitk_gui_qt_segmentationIMGleakage.png", "Leakage correction feature of the Region Growing tool", 12} -
-\imageMacro{"org_mitk_gui_qt_segmentationIMGiconCorrection.png", "Correction Tool", 12} - -The corrector tool is used to perform small corrective changes. The following figure illustrates its use: - - -\imageMacro{"org_mitk_gui_qt_segmentationIMGcorrectionActions.png", "Actions of the Correction tool illustrated.", 12} -
-\imageMacro{"org_mitk_gui_qt_segmentationIMGiconFillErase.png", "Fill and Erase Tools", 12} - -The Fill Tool works by filling a hole surrounded by the active label, at the clicked position. If you click outside the -hole (but yet inside the label) all holes found surrounded by the active label will be filled. - -The Erase Tool removes a connected region of the active label around the clicked position. - -\imageMacro{"org_mitk_gui_qt_segmentationIMGiconLiveWire.png", "LiveWire Tool", 12} - -The LiveWire tool acts as a magnetic lasso with a contour snapping to edges of objects. - -\imageMacro{"org_mitk_gui_qt_segmentationIMGLiveWireUsage.png", "Steps for using LiveWire Tool", 12} - - - -The contour will be transferred to the active label when the tool is deactivated. -\imageMacro{"org_mitk_gui_qt_segmentationIMGiconFastMarching2D.png", "FastMarching Tool", 12} - -The FastMarching tool ... - -\subsection org_mitk_gui_qt_segmentationUserManualInterpolation Interpolation - -Segmenting modern CT and MR volumes is very time-consuming, because structures of interest can easily -cover a range of 50 or more slices. The Segmentation plugin offers two helpful features for these cases: - - -
- -The 3D interpolation is activated by default when using the manual segmentation tools. That means if you start -contouring, from the second contour onwards, the surface of the segmented area will be interpolated based on the available contours. -The interpolation works with all available manual tools. Please note that this is currently a pure geometrical interpolation, -i.e. image intensity information is not taken into account. With each new contour that the user traces, the interpolation result -will improve, but the more contours you provide the longer the recalculation will take. To optimize the interpolation result you -should try to provide sparse contours in arbitrary oriented planes. Generating parallel contours along a given direction is not -a good approach. During interpolation recalculation, the generated surface blinks in yellow/white. When the interpolation -has finished the surface is shown yellow with a small opacity. Additional to the surface, black contours are shown in the 3D render -window. They mark the positions of all the drawn contours which were used for the interpolation. You can navigate between the drawn -contours by clicking on the „Position“ - Nodes in the Data Manager which are located below the active segmentation. If you don't -want to see these nodes just unckeck 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. - -\imageMacro{"org_mitk_gui_qt_segmentation3DInterpolationWrongRight.png", "3D Interpolation HowTo", 12} - -Finally, you can accept the interpolation result by clicking the "Accept" - button below the toolbox. The region inside the surface is -assigned to the active label. - -
-The 2D Interpolation creates suggestions for extending the active label into neighboring slices provided - - -Interpolated suggestions are displayed as contours with the same color as the active label. To accept an interpolation suggestion -in a single slice, click the "Accept" button. You can also accept all interpolated suggestions at once in a -given window, by pressing the "Accept All" button. - -\imageMacro{"org_mitk_gui_qt_segmentation2DInterpolation.png", "2D Interpolation", 12} - -\section org_mitk_gui_qt_segmentationUserManualOrganSegmentation Organ Segmentation - -\note This feature is only available in our 3M3 Demo Application (http://www.mint-medical.de/productssolutions/mitk3m3/mitk3m3/#downloads) but not in the open source part of MITK - -The manual contouring described above is a fallback option that will work for any kind of images and structures of interest. -However, manual contouring is very time-consuming and tedious. -This is why a major part of image analysis research is working towards automatic segmentation methods. -The Segmentation View comprises a number of easy-to-use tools for segmentation of CT images (Liver) and MR image (left ventricle and wall, left and right lung). - -\subsection org_mitk_gui_qt_segmentationUserManualOrganSegmentation1 Liver on CT Images - -On CT image volumes, preferably with a contrast agent in the portal venous phase, the Liver tool will fully automatically analyze and segment the image. -All you have to do is to load and select the image, then click the "Liver" button. -During the process, which takes a minute or two, you will get visual progress feedback by means of a contour that moves closer and closer to the real liver boundaries. - -\subsection org_mitk_gui_qt_segmentationUserManualOrganSegmentation2 Heart, Lung, and Hippocampus on MRI - -While liver segmentation is performed fully automatic, the following tools for segmentation of the heart, the lungs, and the hippocampus need a minimum amount of guidance. -Click one of the buttons on the "Organ segmentation" page to add an average %model of the respective organ to the image. -This %model can be dragged to the right position by using the left mouse button while holding down the CTRL key. -You can also use CTRL + middle mouse button to rotate or CTRL + right mouse button to scale the %model. - -Before starting the automatic segmentation process by clicking the "Start segmentation" button, try placing the %model closely to the organ in the MR image -(in most cases, you do not need to rotate or scale the %model). -During the segmentation process, a green contour that moves closer and closer to the real liver boundaries will provide you with visual feedback of the segmentation progress. - -The algorithms used for segmentation of the heart and lung are method which need training by a number of example images. -They will not work well with other kind of images, so here is a list of the image types that were used for training: - - -\subsection org_mitk_gui_qt_segmentationUserManualOrganSegmentation99 Other Organs - -As mentioned in the Heart/Lung section, most of the underlying methods are based on "training". -The basic algorithm is versatile and can be applied on all kinds of segmentation problems where the structure of interest is topologically like a sphere (and not like a torus etc.). -If you are interested in other organs than those offered by the current version of the Segmentation view, -please contact our research team. - -\subsection org_mitk_gui_qt_segmentationUserManualLesionSegmentation Lesion Segmentation - -\note This feature is only available in our 3M3 Demo Application (http://www.mint-medical.de/productssolutions/mitk3m3/mitk3m3/#downloads) but not in the open source part of MITK - -Lesion segmentation is a little different from organ segmentation. Since lesions are not part of the healthy body, they sometimes have a diffused border, -and are often found in varying places all over the body. -The tools in this section offer efficient ways to create 3D segmentations of such lesions. - -The Segmentation View currently offers support for enlarged lymph nodes. - -To segment an enlarged lymph node, find a more or less central slice of it, activate the "Lymph Node" tool and draw a rough contour on the inside of the lymph node. -When releasing the mouse button, a segmentation algorithm is started in a background task. The result will become visible after a couple of seconds, but you do not have to wait for it. -If you need to segment several lymph nodes, you can continue to inspect the image right after closing the drawn contour. - -If the lymph node segmentation is not to your content, you can select the "Lymph Node Correction" tool and drag %parts of the lymph node surface towards the right position (works in 3D, not slice-by-slice). -This kind of correction helps in many cases. -If nothing else helps, you can still use the pure manual tools as a fallback. - -\section org_mitk_gui_qt_segmentationUserManualOperationsOnLabels Operations on Labels +\section org_mitk_views_multilabelsegmentationUserManualOperationsOnLabels Operations on Labels Depending on your selection in the Label Table , several actions are offered: -\subsection org_mitk_gui_qt_segmentationUserManualOperationsOnSingleSelection Single Label Selection +\subsection org_mitk_views_multilabelsegmentationUserManualOperationsOnSingleSelection Single Label Selection If you right click on any label in the table, a menu will pop-up offering the following actions to be performed on the selected label: -\imageMacro{"org_mitk_gui_qt_segmentationIMGLabelTableSingleSelectionContextMenu.png", "Context menu for single label selection", 12} +\imageMacro{"org_mitk_views_multilabelsegmentationIMGLabelTableSingleSelectionContextMenu.png", "Context menu for single label selection", 12} -\subsection org_mitk_gui_qt_segmentationUserManualOperationsOnMultipleSelection Multiple Label Selection +\subsection org_mitk_views_multilabelsegmentationUserManualOperationsOnMultipleSelection Multiple Label Selection If more than one label is selected, a different menu will show up: -\imageMacro{"org_mitk_gui_qt_segmentationIMGLabelTableMultipleSelectionContextMenu.png", "Context menu for multiple label selection", 12} +\imageMacro{"org_mitk_views_multilabelsegmentationIMGLabelTableMultipleSelectionContextMenu.png", "Context menu for multiple label selection", 12} -\section org_mitk_gui_qt_segmentationUserManualSegmentationUtilities Segmentation Utilities - -The Segmentation Utilities view ... - -One is the surface masking utility. It is used for create a new label from a surface. The surface is used as a "mask": the region inside -the surface is assigned a new label. - -\imageMacro{"org_mitk_gui_qt_segmentationIMGsurfacemask.png", "Surface masking utility", 12} - -Select the image and the surface in the corresponding drop-down boxes (both are selected automatically if there is just one image and one surface) - -\section org_mitk_gui_qt_segmentationUserManualTechnicalDetail Technical Information for Developers - -A list of properties can be found at \subpage MultiLabelSegmentationPropertiesPage. -For technical specifications see : \subpage QmitkSegmentationTechnicalPage and for information on the extensions of the tools system : \subpage toolextensions. - */ diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_gui_qt_segmentation2DInterpolation.png b/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_gui_qt_segmentation2DInterpolation.png deleted file mode 100644 index 09ed1e4f17..0000000000 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b/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/segmentationFromSurfaceBefore.png deleted file mode 100644 index d12d44fb9f..0000000000 Binary files a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/segmentationFromSurfaceBefore.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/doxygen/MultiLabelSegmentationProperties.dox b/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/doxygen/MultiLabelSegmentationProperties.dox deleted file mode 100644 index e4d8347623..0000000000 --- a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/doxygen/MultiLabelSegmentationProperties.dox +++ /dev/null @@ -1,10 +0,0 @@ -/** -\page MultiLabelSegmentationPropertiesPage The Segmentation properties - -These properties control how a segmentation is rendered: - - -*/ \ No newline at end of file