New Segment Editor effect: Local threshold

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:

  • Masking
  • GrowCut
  • WaterShed

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.



I found it a very nice feature. However, while trying to use it, i found that after selecting a threshold and ctrl plus left click-it doesn’t do anything. I mean no filling is done. Is there anything I am missing?


Local threshold effect attempts to reduce leaking and separates the structure that you clicked on by eroding the thresholded area by the “feature size” parameter.

If the area under the mouse would be eroded away, then the local threshold effect will not find the structure. If you reduce the “feature size” parameter, or make sure to click in a non-eroded region, than it should help find the structure.

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Late reply and perhaps this is documented somewhere else, but on MacOS it is command-click to add, not control-click.

Most excellent feature, by the way. Thanks!