Overview of the most important is provided below. There are many modules in 3D Slicer for manipulating segmentations. Each layer is stored internally as a separate 3D volume, and one volume may be shared between many non-overlapping segments to conserve memory.
To store overlapping segments in binary labelmaps, segments are organized into layers. In 3D Slicer, overlapping between segments is allowed. Most software that use this representation, store all segments in a single 3D array, therefore each voxel can belong to a single segment: segments cannot overlap.
The master representation is the only editable representation, it is the only one that is stored when saving to file, and all other representations are computed from it automatically.īinary labelmap representation is probably the most commonly used representation because this representation is the easiest to edit. One representation is designated as the master representation (marked with a “gold star” on the user interface). Binary labelmapĮach segment stored in multiple representations. There is no one single representation that works well for everything: each representation has its own advantages and disadvantages and used accordingly. Segments may overlap each other in space.Ī region can be represented in different ways, for example as a binary labelmap (value of each voxel specifies if that voxel is inside or outside the region) or a closed surface (surface mesh defines the boundary of the region). Each segment has a number of properties, such as name, preferred display color, content description (capable of storing standard DICOM coded entries), and custom properties. A segmentation node consists of multiple segments.Ī segment specifies region for a single structure. Result of a segmentation is stored in segmentation node in 3D Slicer. Segment Editor module offers a wide range of segmentation methods.
Segmentation may be performed manually, for example by iterating through all the slices of an image and drawing a contour at the boundary but often semi-automatic or fully automatic methods are used. It is a very common procedure in medical image computing, as it is required for visualization of certain structures, quantification (measuring volume, surface, shape properties), 3D printing, and masking (restricting processing or analysis to a specific region), etc. Segmentation of images (also known as contouring or annotation) is a procedure to delinate regions in the image, typically corresponding to anatomical structures, lesions, and various other object space.
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