# 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