This can be used for drawing inside a specific region or split a segment into multiple segments.Įditable intensity range: Changes will be limited to areas where the master volume’s voxels are in the selected intensity range. Masking: These options allow you to define the editable areas and whether or not certain segments can be overwritten.Įditable area: Changes will be limited to the selected area. By default the last 10 states are remembered. This is useful for experimentation and error correction. Undo/Redo: The module saves state of segmentation before each effect is applied. Options: Options for the selected effect will be displayed here. See below for more information about each effect. To customize visualization: either open the slice view controls (click on push-pint and double-arrow icons at the top of a slice viewer) or go to Segmentations module.Ĭolor swatch: set color and assign segment to standardized terminology.Įffects: Select the desired effect here. Segments table: Displays list of all segments.Įye icon: Toggle segment’s visibility. Set Smoothing factor to 0.1 for weak smoothing and 0.5 or larger for stronger smoothing. Setting Smoothing factor to 0 disables smoothing, making updates much faster.
#Binary editor reducing fuel update
To change surface creation parameters: go to Segmentations module, click Update button in Closed surface row in Representations section, click Binary labelmap -> Closed surface line, double-click on value column to edit a conversion parameter value. When turned off, the conversion is not ongoing so the segmentation process is faster. When turned on the surface is created and updated automatically as the user is segmenting. Remove segment: Select the segment you would like to delete then click Remove segment to delete from the segmentation.Ĭreate Surface: Display your segmentation in the 3D Viewer. If the “Pad output” is checked, the extent will be expanded so that it contains both the existing segments and the new reference geometry.Īdd segment: Add a new segment to the segmentation and select it. If the new geometry will crop a region from the existing segments, a warning icon will be displayed beside the “Pad output” checkbox. To specify an arbitrary extens, an ROI (region of interest) node can be created and selected as source geometry. To make changes to the geometry (make the extent larger, the resolution finer, etc.) click “Specify geometry” button next to the master volume selector, select a “Source geometry” node that will be used as a basis for the new geometry, adjust parameters, and click OK. Note: changing the master volume does not affect the segmentation’s labelmap representation geometry. The master volume can be changed at any time during the segmentation process. The master volume is used by all editor effects that uses intensity of the segmented volume (e.g., thresholding, level tracing). The master volume that is selected the very first time after the segmentation is created is used to determine the segmentation’s labelmap representation geometry (extent, resolution, axis directions, origin). Master volume: Choose the volume to segment. Segmentation: Choose the segmentation to edit They are intended to allow two-handed editing, where on hand is on the mouse and the other hand uses the keyboard to switch modes. The following keyboard shortcuts are active when you are in the Segment Editor module. Additional references to non-trivial algorithms used in Segment Editor effects are provided below, in the documentation of each effect. Fichtinger, “Polymorph segmentation representation for medical image computing”, Computer Methods and Programs in Biomedicine, Volume 171, p19-26, 2019 ( pdf, DOI). To cite the Segment Editor in scientific publications, you can cite 3D Slicer and the Segment Editor paper: Cs. Segment Editor does not edit labelmap volumes or models, but segmentations can be easily converted to/from labelmap volumes and models using the Import/Export section of Segmentations module. The module offers editing of overlapping segments, display in both 2D and 3D views, fine-grained visualization options, editing in 3D views, create segmentation by interpolating or extrapolating segmentation on a few slices, editing on slices in any orientation. Some of the tools mimic a painting interface like photoshop or gimp, but work on 3D arrays of voxels rather than on 2D pixels. This is a module is for specifying segments (structures of interest) in 2D/3D/4D images.
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