diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/QmitkMultiLabelSegmentation.dox b/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/QmitkMultiLabelSegmentation.dox index c0f9d94840..bfd845dd11 100644 --- a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/QmitkMultiLabelSegmentation.dox +++ b/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/QmitkMultiLabelSegmentation.dox @@ -1,118 +1,99 @@ /** \page org_mitk_views_multilabelsegmentation The Multilabel Segmentation -\imageMacro{"multilabelsegmentation-dox.svg", "Icon of the MultiLabelSegmentation Plugin", 12} +\imageMacro{multilabelsegmentation_utilities.svg, "Icon of the Multilabel Segmentation Utilities Plugin", 5.00} -The difference between a binary and a multi-label segmentation is that a multi-label segmentation can not only contain more than one label but also more than one layer. This allows you to create different labels for different regions of interest encapsulated in one single image. The difference between labels and layers is that labels on one layer cannot overlap but labels on different layers can. -
-The Multilabel Segmentation plugin consists of two views which can be used for: +The Multilabel Segmentation plugin consists of one view which can be used for: -Hereinafter, a description is given on how multi-label segmentations can be created and modified. Please refer to \ref org_mitk_views_segmentation for a description of the general segmentation tools. +Hereinafter, a description is given on how multilabel segmentations can be modified. +Please refer to \ref org_mitk_views_segmentation for a description of the general segmentation tools. \tableofcontents -\section org_mitk_views_multilabelsegmentationUserManualCreateOpenSaveImportAdd Data Selection +\section org_mitk_views_multilabelsegmentationutilitiesoverview Overview -In the 'MultiLabel Segmentation' view you can first select an image. Thereafter, you can either create a new segmentation session by pressing the symbol right to the selection widget or select an existing one. - -\imageMacro{"org_mitk_views_multilabelsegmentationIMGtoolbar.png", "Data selection",12} - - -\section org_mitk_views_multilabelsegmentationUserManualLayerTable Segmentation Layers -Once you started a segmentation session you can add or delete different layers. You can use the layers independently and switch layers by the left and right arrows. - - -\imageMacro{"org_mitk_views_multilabelsegmentationIMGlayerManager.png", "Layer selection",12} - -\subsection 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 radiotherapy 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 accommodate all these segmentations in separate labels because they all occupy different anatomical 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 lesion you would like to treat. - -\section org_mitk_views_multilabelsegmentationUserManualLabelTable Segmentation Labels - -For each layer, you can add one or more labels. Pressing the double arrow on the right, all created labels are shown in the 'Lable Table'. The following label properties are available: +The Multilabel Segmentation Utilities Plugin allows to postprocess existing segmentations. Currently five different operations exist: +\imageMacro{QmitkMultiLabelSegmentationUtilities_Overview.png, "The Multilabel Segmentation Utilities View",16.00} -\imageMacro{"org_mitk_views_multilabelsegmentationIMGlabeltable.png", "The 'Label Table' shows all labels in the current segmentation session", 12} - -\subsection org_mitk_views_multilabelsegmentationUserManualLabelCreation Creating a New Label +\section org_mitk_views_multilabelsegmentationutilitiesdataselection Data Selection -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. +All postprocessing operations provide one or more selection widgets, which allow to select the data for the operation. +\section org_mitk_views_multilabelsegmentationutilitiesbooleanoperations Boolean operations -\subsection org_mitk_views_multilabelsegmentationUserManualLabelPresets Saving and Loading Label Set Presets +Boolean operations allow to perform the following fundamental operations on two segmentations: -Label set presets are useful to share a certain style or scheme between different segmentation sessions or to provide templates for new segmentation sessions. - -The properties of all labels in all layers like their names, colors, and visibilities are saved as a label set preset by clicking on the 'Save label set preset' button. -Label set presets are applied to any segmentation session by clicking on the 'Load label set preset' button. -If a label for a certain value already exists, its properties are overridden by the preset. -If a label for a certain value does not yet exist, an empty label with the label properties of the preset is created. -The actual segmentations of labels are unaffected as label set presets only store label properties. - - -\subsection 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 can be time-consuming. -The 'Label Search' edit box allows for quickly finding the label you want. Just start writing its name and you will get assistance for completing its name. If the label you were searching is found, press 'enter' and it will become the active one. + +The selected segmentations must have the same geometry (size, spacing, ...) in order for the operations to work correctly. +The result will be stored in a new data node as a child node of the first selected segmentation. -\subsection org_mitk_views_multilabelsegmentationUserManualLabelEditing Label Editing +\imageMacro{QmitkMultiLabelSegmentationUtilities_BooleanOperations.png,"Boolean operations",6.00} -Here the actual segmentation takes place. First of all, you have to select the active label by clicking on the corresponding row in the 'Label Table'. Note that only one label can be active at the time. Then you can select segmentation tool in the toolbox. +\section org_mitk_views_multilabelsegmentationutilitiescontourtoimage Contour to image -\imageMacro{"org_mitk_views_multilabelsegmentationIMGSegmentationToolbox.png", "Segmentation toolbox", 12} +Contour to image allows to create a segmentation out of a given contour-model. +The operation requires a contour model set and a reference image. +The created segmentation image will have the same geometrical properties like the reference image (dimension, size and Geometry3D). +\imageMacro{QmitkMultiLabelSegmentationUtilities_ContourToImage.png,"Contour to image",6.00} -\note Not all segmentation tools can be found here. This is because some of the semi-automatic tools can not be applied in case of multiple labels. +\section org_mitk_views_multilabelsegmentationutilitiesimagemasking Image masking -\subsection org_mitk_views_multilabelsegmentationUserManualOperationsOnLabels Operations on Labels +Image masking allows to mask an image with either an existing segmentation or a surface. +The operation requires an image and a binary image mask or a surface. +The result will be an image containing only the pixels that are covered by the respective mask. +Depending on the selected mode ("make output binary" or "overwrite foreground" / "overwrite background") +the result will be a simple image or a binary image. -Depending on your selection in the 'Label Table', several actions are offered: +\imageMacro{QmitkMultiLabelSegmentationUtilities_ImageMasking.png,"Image masking",6.00} -\subsubsection org_mitk_views_multilabelsegmentationUserManualOperationsOnSingleSelection Single Label Selection +\section org_mitk_views_multilabelsegmentationutilitiesmorphologicaloperations Morphological operations -If you right click on any label in the table, a pop-up menu offers the following actions to be performed on the selected label: +Morphological operations are applied to a single segmentation image. Based on a given structuring element the underlying segmentation will be modfied. +The plugin provides a ball and a cross as structuring elements. The follow operations are available: -\imageMacro{"org_mitk_views_multilabelsegmentationIMGLabelTableSingleSelectionContextMenu.png", "Context menu for single label selection", 12} +\imageMacro{QmitkMultiLabelSegmentationUtilities_MorphologicalOperations.png,"Morphological operations",6.00} -\subsubsection org_mitk_views_multilabelsegmentationUserManualOperationsOnMultipleSelection Multiple Label Selection +\section org_mitk_views_multilabelsegmentationutilitiessurfacetoimage Surface to image -You can select more than one label by shift-click on other labels. If more than one label is selected, different options will appear in the menu: +Surface to image allows to create a segmentation out of a given surface. +The operation requires a surface and a reference image. +The created segmentation image will have the same geometrical properties like the reference image (dimension, size and Geometry3D). +Depending on the selected mode ("make output binary" or "overwrite background") +the result will be a simple image or a binary image. -\imageMacro{"org_mitk_views_multilabelsegmentationIMGLabelTableMultipleSelectionContextMenu.png", "Context menu for multiple label selection", 12} +\imageMacro{QmitkMultiLabelSegmentationUtilities_SurfaceToImage.png,"Surface to image",6.00} - +\section org_mitk_views_multilabelsegmentationutilitiesconverttomultilabel Convert to Multilabel + +Convert to multilabel allows to interpret the pixel values of a given image as label IDs and convert the image content into the respective Multilabel image. +The new segmentation will contain one layer with as many labels as the original image contains different pixel values. +\imageMacro{QmitkMultiLabelSegmentationUtilities_ConvertToMultilabel.png,"Convert to Multilabel",6.00} */ diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/QmitkMultiLabelSegmentationUtilities.dox b/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/QmitkMultiLabelSegmentationUtilities.dox deleted file mode 100644 index 7a44044261..0000000000 --- a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/QmitkMultiLabelSegmentationUtilities.dox +++ /dev/null @@ -1,91 +0,0 @@ -/** -\page org_mitk_views_multilabelsegmentationutilities The Multilabel Segmentation Utilities - -\imageMacro{multilabelsegmentation_utilities.svg,"Icon of the Multilabel Segmentation Utilities Plugin",5.00} - -\imageMacro{QmitkMultiLabelSegmentationUtilities_Overview.png, "The Multilabel Segmentation Utilities View",16.00} - -\tableofcontents - -\section org_mitk_views_multilabelSegmentationUtilitiesOverview Overview - -The Multilabel Segmentation Utilities Plugin allows to postprocess existing segmentations. Currently five different operations exist: - - - -\section org_mitk_views_multilabelSegmentationUtilitiesDataSelection Data Selection - -All postprocessing operations provide one or more selection widgets, which allow to select the data for the operation. - -\section org_mitk_views_multilabelSegmentationUtilitiesBooleanOperations Boolean operations - -Boolean operations allows to perform the following fundamental operations on two segmentations: - - - -The selected segmentations must have the same geometry (size, spacing, ...) in order for the operations to work correctly. -The result will be stored in a new data node as a child node of the first selected segmentation. - -\imageMacro{QmitkMultiLabelSegmentationUtilities_BooleanOperations.png,"Boolean operations",6.00} - -\section org_mitk_views_multilabelSegmentationUtilitiesContourToImage Contour to image - -Contour to image allows to create a segmentation out of a given contour-model. -The operation requires a contour model set and a reference image. -The created segmentation image will have the same geometrical properties like the reference image (dimension, size and Geometry3D). - -\imageMacro{QmitkMultiLabelSegmentationUtilities_ContourToImage.png,"Contour to image",6.00} - -\section org_mitk_views_multilabelSegmentationUtilitiesImageMasking Image masking - -Image masking allows to mask an image with either an existing segmentation or a surface. -The operation requires an image and a binary image mask or a surface. -The result will be an image containing only the pixels that are covered by the respective mask. -Depending on the selected mode ("make output binary" or "overwrite foreground" / "overwrite background") -the result will be a simple image or a binary image. - -\imageMacro{QmitkMultiLabelSegmentationUtilities_ImageMasking.png,"Image masking",6.00} - -\section org_mitk_views_multilabelSegmentationUtilitiesMorphologicalOperations Morphological operations - -Morphological operations are applied to a single segmentation image. Based on a given structuring element the underlying segmentation will be modfied. -The plugin provides a ball and a cross as structuring elements. The follow operations are available: - - - -\imageMacro{QmitkMultiLabelSegmentationUtilities_MorphologicalOperations.png,"Morphological operations",6.00} - -\section org_mitk_views_multilabelSegmentationUtilitiesSurfaceToImage Surface to image - -Surface to image allows to create a segmentation out of a given surface. -The operation requires a surface and a reference image. -The created segmentation image will have the same geometrical properties like the reference image (dimension, size and Geometry3D). -Depending on the selected mode ("make output binary" or "overwrite background") -the result will be a simple image or a binary image. - -\imageMacro{QmitkMultiLabelSegmentationUtilities_SurfaceToImage.png,"Surface to image",6.00} - -\section org_mitk_views_multilabelSegmentationUtilitiesConvertToMultiLabel Convert to Multilabel - -Convert to multilabel allows to interpret the pixel values of a given image as label IDs and convert the image content into the respective Multilabel image. -The new segmentation will contain one layer with as many labels as the original image contains different pixel values. - -\imageMacro{QmitkMultiLabelSegmentationUtilities_ConvertToMultilabel.png,"Convert to Multilabel",6.00} -**/ diff --git a/Plugins/org.mitk.gui.qt.radiomics/documentation/UserManual/QmitkPhenotypingPortalPage.dox b/Plugins/org.mitk.gui.qt.radiomics/documentation/UserManual/QmitkPhenotypingPortalPage.dox index 550c6d9daf..c9afa60b63 100644 --- a/Plugins/org.mitk.gui.qt.radiomics/documentation/UserManual/QmitkPhenotypingPortalPage.dox +++ b/Plugins/org.mitk.gui.qt.radiomics/documentation/UserManual/QmitkPhenotypingPortalPage.dox @@ -1,40 +1,40 @@ /** \page org_mitk_gui_qt_mitkphenotyping The Phenotyping \tableofcontents MITK Phenotyping is a selection of algorithms that can be used to extract image-based phenotypes, for example using a radiomics approach. The software is part of the research of the Division of Medical Image Computing of the German Cancer Research Center (DKFZ). MITK Phenotyping is not intended to be a single application, it is rather a collection of the necessary plugins within the offical MITK releases. The functionality of MITK Phenotyping can be accessed in different ways: Using the graphical interface using the Plugins listed below, using command line applications, or using one of the programming interfaces. \section org_mitk_gui_qt_mitkphenotyping_Tutorials Tutorials \li \subpage org_mitk_views_radiomicstutorial_gui_portal A tutorial on how to use the grapical interface of MITK Phenotying \section org_mitk_gui_qt_mitkphenotyping_Views Views \subsection sub2 Specific Views: Views that were developed with the main focus on Radiomics. They still might be used in other use-cases as well: \li \subpage org_mitk_views_radiomicstransformationview : Image transformations like Resampling, Laplacian of Gaussian, and Wavelet Transformations \li \subpage org_mitk_views_radiomicsmaskprocessingview : Processing and Cleaning of Masks \li \subpage org_mitk_views_radiomicsarithmetricview : Processing images using mathematical operations \li \subpage org_mitk_views_radiomicsstatisticview : Calculate Radiomics Features \subsection sub1 Non-Specific Views: This section contains views that are included within MITK Phenotyping, but were developed with a broader application in mind. \li \ref org_mitk_views_basicimageprocessing : Deprecated plugin for performing different image-related tasks like subtraction, mutliplaction, filtering etc. \li \ref org_mitk_views_matchpoint_algorithm_browser : Selection of MatchPoint (Registration) Algorithm \li \ref org_mitk_views_matchpoint_algorithm_control : Configuring and Controlling MatchPoint (Registration) Algorithm \li \ref org_mitk_views_matchpoint_evaluator : Evaluate the Registration performance using MatchPoint \li \ref org_mitk_views_matchpoint_manipulator : Adapt a registration calculated using MatchPoint \li \ref org_mitk_views_matchpoint_mapper : Apply a MatchPoint Registration to a specific image \li \ref org_mitk_views_matchpoint_visualizer : Visualize a Registration obtained with MatchPoint -\li \ref org_mitk_views_multilabelsegmentation : Create and editing of Multilabel-Segmentations. -\li \ref org_mitk_views_segmentation : Create simple segmentations -\li \ref org_mitk_views_segmentationutilities : Utilities for the processing of simple segmentations. +\li \ref org_mitk_views_segmentation : Creating Multilabel Segmentations +\li \ref org_mitk_views_segmentationutilities : Utilities for the processing of simple segmentations +\li \ref org_mitk_views_multilabelsegmentation : Utilities for the processing of Multilabel Segmentations \section radiomics_miniapps MiniApps (Command line Tools) \li \subpage MiniAppExplainPage Explanation of the Command Line App concept in MITK \li \subpage mitkBasicImageProcessingMiniAppsPortalPage : List of common preprocessing MiniApps \li \subpage mitkClassificationMiniAppsPortalPage : (Incomplete) list of MITK Classification MiniApps */