What Enhancement Actually Does#

Enhancers modify the detect_mat accessor — the grayscale representation that detectors consume. They never touch rgb or gray, preserving the original image data for visualization and color measurements.

Why Enhance?#

Raw plate images often have properties that confuse detectors:

  • Noise — random pixel variation that creates false positives

  • Low contrast — faint colonies barely distinguishable from agar

  • Uneven illumination — brightness gradients across the plate

  • Texture — agar surface patterns that mimic colony edges

Enhancement addresses these problems by transforming detect_mat into a version where colonies stand out more clearly.

Categories of Enhancement#

Smoothing (Noise Reduction)#

Reduce random variation while preserving colony boundaries.

  • BlurGauss — isotropic smoothing; fast but blurs edges

  • MedianFilter — removes salt-and-pepper noise; preserves edges better

  • LocalEdgeDenoise — smooths within regions; preserves edges explicitly

  • DenoiseBlockMatch (BM3D) — state-of-the-art block-matching denoising

Contrast Enhancement#

Increase the separation between colony and background intensities.

  • EnhanceLocalContrast — local adaptive histogram equalization; handles spatially varying contrast

  • ContrastStretching — linear remapping to fill the dynamic range

  • SharpenEdgeGauss — sharpens edges by subtracting a blurred version

Illumination Correction#

Remove large-scale brightness gradients.

  • FlattenIllumination — frequency-domain separation of illumination and reflectance

  • SubtractGaussian — subtracts a heavily blurred background estimate

  • SubtractRollingBall — morphological background estimation

Structural Enhancement#

Enhance specific morphological features.

  • FocusEdgeFrangi — enhances tubular structures (hyphae, branches)

  • FocusEdgeSobel — highlights edges

  • FocusEdgePhase — illumination-invariant edge detection

  • FocusEdgeMonogenicPhase — the same illumination invariance without the orientation sweep, via the monogenic signal. Cheaper and isotropic; use it when colony edges have no preferred direction. Its output="orientation" / "feature_type" modes are diagnostic angle maps, not detection inputs.

  • FocusEdgeColorPhase — runs the monogenic chain on three colour channels and fuses them, so a channel with amplitude but no phase agreement can veto a spurious luminance edge. It reads rgb, not detect_mat, which makes it a pipeline source: any enhancer placed before it has no effect. Reach for it on filamentous plates. On round-colony plates, FocusEdgeMonogenicPhase on luminance measurably localizes boundaries better than any of its fusion modes, so colour buys nothing there. Rejects achromatic images outright.

Stacking Enhancers#

Enhancers compose linearly — each reads detect_mat, modifies it, and writes it back. Order matters:

Note

One exception. FocusEdgeColorPhase reads image.rgb, not detect_mat, because colour phase congruency is defined on colour. It is a source: it discards whatever detect_mat held and writes a fresh map. Anything upstream of it in the chain is wasted work. Put it first, or not at all.

  1. Denoise first — reduce noise before amplifying contrast

  2. Correct illumination — normalize brightness before thresholding

  3. Enhance contrast — maximize colony/background separation last

A typical preprocessing chain: BlurGauss → FlattenIllumination → EnhanceLocalContrast.

The Enhancement ↔ Detection Interface#

detect_mat  ──[Enhancer 1]──→  detect_mat  ──[Enhancer 2]──→  detect_mat
                                                                    │
                                                              [Detector]
                                                                    │
                                                              objmask, objmap

This clean interface means you can swap any enhancer without affecting the detector, and vice versa. The pipeline model makes this experimentation easy.