Medical Imaging Interaction Toolkit  2021.10.00
Medical Imaging Interaction Toolkit
The Multilabel Segmentation
Icon of the MultiLabelSegmentation Plugin

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:

  • manual and (semi-)automatic segmentation of anatomical and pathological structures in medical images via the Multilabel Segmentation View
  • multilabel segmentation postprocessing via The Multilabel Segmentation Utilities

Hereinafter, a description is given on how multi-label segmentations can be created and modified. Please refer to The Segmentation View for a description of the general segmentation tools.

Data Selection

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.

Data selection

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.

Layer selection

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.

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:

  • Name: the name of the label. Can be a predefined one or any other.
  • Locked: whether the label is locked or editable. A locked label cannot be overwritten by another.
  • Color: the color of the label.
  • Visible: whether the label is currently visible or hidden.
The 'Label Table' shows all labels in the current segmentation session

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.

Saving and Loading Label Set Presets

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.

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.

Label Editing

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.

Segmentation toolbox
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.

Operations on Labels

Depending on your selection in the 'Label Table', several actions are offered:

Single Label Selection

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:

  • Rename... : change the name and/or color of the selected label.
  • Remove... : delete the selected label.
  • Erase... : only clear the contents of the selected label.
  • Merge... : merge two labels by selecting a second label.
  • Random color : assign a random color to the label.
  • View only : make all labels except the current selected label invisible.
  • View/Hide all : make all labels visible / invisible
  • Lock/Unlock all : lock or unlock all labels.
  • Create surface : generate a surface out of the selected label.
  • Create mask : generate a mask out of the selected label. A mask is a binary image with "1" inside and "0" outside.
  • Create cropped mask : generate a binary mask out of the selected label. Crop changes the extent of the resulting image to the extent of the label.
Context menu for single label selection

Multiple Label Selection

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:

Context menu for multiple label selection
  • Merge selection on current label : transfer the contents of the selected labels in the 'Label Table' into the current one.
  • Remove selected labels : delete the selected labels.
  • Erase selected labels : only clear the contents of the selected labels.