Refinement Strategies

After detection, the raw binary mask and labeled object map often contain artifacts. Refiners clean up these artifacts without re-running detection.

Common Artifacts

Artifact	Cause	Refiner
Border objects	Partial colonies at image edges	BorderObjectRemover
Small fragments	Noise, agar texture	SmallObjectRemover
Holes in masks	Uneven colony interior intensity	MaskFill
Jagged edges	Threshold quantization	MaskOpener, MaskCloser
Touching colonies merged	Threshold too low	SeparateObjects
One colony fragmented	Threshold too high	NearestNeighborMerger, MaskCloser
Multiple detections per well	Over-segmentation in grid plates	ReduceMultipleGridObjects
Oversized objects	Merged colonies spanning wells	GridOversizedObjectRemover

Refinement Order

The recommended refinement sequence:

1. BorderObjectRemover — remove partial edge colonies first

2. SmallObjectRemover — remove noise fragments

3. MaskOpener — smooth boundaries and break thin bridges

4. MaskFill — fill interior holes

5. Grid-specific refiners — align, reduce multiples, remove oversized

This order ensures that each refiner operates on progressively cleaner masks.

Morphological Refiners

Morphological operations use a structuring element (footprint) to reshape mask boundaries.

• MaskOpener (erosion → dilation) — removes small protrusions, breaks thin bridges between touching colonies

• MaskCloser (dilation → erosion) — fills small gaps, bridges narrow breaks in fragmented colonies

• MaskDilator — expands mask boundaries outward

• MaskEroder — shrinks mask boundaries inward

• MaskFill — fills enclosed holes using binary flood fill

The width parameter controls the footprint size. Larger footprints produce more aggressive changes.

Grid-Specific Refiners

These refiners use grid position information and are only available for GridImage:

• GridAligner — rotates the image to align the grid

• GridOversizedObjectRemover — removes objects larger than expected for a single well

• ReduceMultipleGridObjects — when multiple objects are in one grid section, keeps only the most prominent

• MergeGridObj — merges all objects within a grid section into one

Tuning Strategy

Start with the default refiner chain in a prefab pipeline. If the results are not satisfactory:

1. Check the overlay — identify which artifact type persists

2. Add or adjust the corresponding refiner

3. Adjust min_size, width, or border_size parameters

4. Re-run and compare