Local threshold, a new semi-automatic segmentation method, has been added to the Segment Editor. It is available in both the 4.11.0 and 4.10.2 releases through the SegmentEditorExtraEffects extension. This effect adds connected voxels to segments that are within a specified threshold, and attempts to prevent leaks into other structures through small connecting regions. The result is similar to that of the “Level trace” effect in that it delineates a region within a certain threshold value, however this effect is applied in 3D.
The initial behavior is similar to the threshold effect. Users can specify a threshold range manually, or by drawing on the image to create a histogram (see info here). Instead of clicking “Apply”, CTRL+clicking on a specific region performs a flood fill using one of 3 algorithms, adding the structure to the current segment:
Two additional parameters are also available to prevent leaks:
- Feature size: Used to separate structures that are connected by regions smaller than the size specified
- ROI: Only voxels within the region of interest will be filled
Suggestions and feedback are welcome.
Development was funded in part by CANARIE’s Research Software Program, OpenAnatomy, and Brigham and Women’s Hospital through NIH grant R01MH112748.