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Isolate Largest Feature (Identify Sample)

Group (Subgroup)

Processing (Cleanup)


Often when performing a serial sectioning experiment (especially in the FIB-SEM), the sample is overscanned resulting in a border of bad data around the sample. This Filter attempts to identify the sample within the overscanned volume. The Filter makes the assumption that there is only one contiguous set of Cells that belong to the sample. The Filter requires that the user has already thresheld the data to determine which Cells are good and which are bad. The algorithm for the identification of the sample is then as follows:

  1. Search for the largest contiguous set of good Cells. (This is assumed to be the sample)
  2. Change all other good Cells to be bad Cells. (This removes the "speckling" of what was thresheld as good data in the outer border region)

If Fill Holes is set to true: 3. Search for the largest contiguous set of bad Cells. (This is assumed to be the outer border region) 4. Change all other bad Cells to be good Cells. (This removes the "speckling" of what was thresheld as bad data inside of the sample).

Note: if there are in fact "holes" in the sample, then this Filter will "close" them (if Fill Holes is set to true) by calling all the Cells "inside" the sample good. If the user wants to reidentify those holes, then reuse the threshold Filter with the criteria of GoodVoxels = 1 and whatever original criteria identified the "holes", as this will limit applying those original criteria to within the sample and not the outer border region.

Name Description
Good dataset to use this filter
NOT a good data set to use because there is no overscan of the sample.


Name Type Description
Fill Holes in Largest Feature bool Whether to fill holes within sample after it is identified

Required Geometry


Required Objects

Kind Default Name Type Component Dimensions Description
Cell Attribute Array Mask bool (1) Mask array defining what is sample and what is not

Created Objects


Example Pipelines

  • (10) SmallIN100 Full Reconstruction
  • INL Export
  • (03) SmallIN100 Alignment

Please see the description file distributed with this Plugin

DREAM.3D Mailing Lists

If you need more help with a Filter, please consider asking your question on the DREAM.3D Users Google group!