Measurement Metrics and Their Biological Meaning#

PhenoTypic’s measurement operations extract quantitative features from detected colonies. This page explains what each metric means biologically and when to use it.

For how to apply each metric — which to report directly vs. use as a classifier feature — see Measurement Classification: Phenotypes vs. Features.

Size Metrics (MeasureSize)#

Metric	Unit	Biological meaning
Area	pixels	Colony size; proxy for biomass or growth
IntegratedIntensity	sum of pixel values	Total pigmentation; proxy for metabolic output

Area is the most commonly used growth metric. For calibrated images, convert pixels to physical units (mm²) using the known pixel pitch.

Shape Metrics (MeasureShape)#

Metric	Range	Biological meaning
Circularity	0–1	How round the colony is (1 = perfect circle). Irregular shapes suggest stress, mutation, or sectoring.
Solidity	0–1	Ratio of area to convex hull area. Low solidity indicates lobed or branching morphology.
Eccentricity	0–1	Elongation (0 = circular, ~1 = very elongated). Elevated in filamentous or swarming colonies.
Perimeter	pixels	Colony boundary length. Increases faster than area for irregular shapes.
MajorAxisLength / MinorAxisLength	pixels	Fitted ellipse dimensions. The ratio indicates elongation.
Compactness	≥1	Perimeter² / (4π × Area). Equals 1 for a perfect circle; increases with irregularity.

Shape metrics are particularly useful for distinguishing wild-type from mutant morphology, or for detecting contamination.

Intensity Metrics (MeasureIntensity)#

Metric	Biological meaning
MeanIntensity	Average colony brightness; correlates with pigment concentration
MedianIntensity	Robust center of the intensity distribution; less affected by bright/dark spots
StandardDeviationIntensity	Internal color variation; high values suggest heterogeneous pigmentation or sectoring
MinimumIntensity / MaximumIntensity	Intensity extremes within the colony
CoefficientVarianceIntensity	Normalized variation (StdDev / Mean); comparable across colonies of different brightness

Color Metrics (MeasureColor)#

Color measurements report compact, outlier-resistant colorimetric summaries rather than a per-channel statistical suite. The default output covers two perceptually meaningful spaces, CIE L*a*b* and HSV.

Two robust center colors (CIE L*a*b*). L*a*b* is designed so Euclidean distance approximates perceived color difference (ΔE76).

L*GeoMedian, a*GeoMedian, b*GeoMedian — the ΔE76 (Euclidean) geometric median of the colony’s pixels. The multivariate median (breakdown point 0.5), so specular highlights, agar bleed-through, and debris cannot drag the center color.
L*Medoid, a*Medoid, b*Medoid — the ΔE2000 medoid: the single real colony pixel minimizing total ΔE2000 to all other pixels. Because ΔE2000 is not a true metric, a medoid (which needs no metric axioms) is used instead of a geometric median, and the result is always an actual colony color.

Within-colony color consistency (ΔE2000, from the medoid). A perceptually-corrected uniformity profile:

DeltaE2000MedianFromMedoid — robust “perceptual MAD.”
DeltaE2000MeanFromMedoid — the color-science uniformity standard.
DeltaE2000P95FromMedoid — near-worst-case deviation; flags sectoring and contamination without being dominated by a single stray pixel.
LabTotalVariance — the trace of the L*a*b* covariance (var L* + var a* + var b*), a single Euclidean spread scalar.

Robust HSV. Because hue is circular and HSV is not perceptually uniform, each pixel is embedded into Cartesian cone coordinates before the robust center is computed:

HueRobustMean, SaturationRobustMean, ValueRobustMean — the cone-embedded geometric-median center converted back to H, S, V (circular-correct; unreliable hue at low saturation collapses toward the achromatic axis automatically).
HSVConeVariance — the trace of the cone-Cartesian covariance.

Plot swatch. MedoidColorHex is the sRGB hex string of the ΔE2000 medoid color, intended for visualization only — it is never used as a numeric measurement or analysis input.

These metrics are essential for:

Quantifying pigmentation differences between strains
Detecting sectoring (regions of different color within a colony)
Normalizing color across imaging sessions (after ColorCorrector)

CIE XYZ and xy chromaticity remain available as opt-in legacy per-channel suites (MeasureColor(include_XYZ=True), MeasureColor(include_xy=True)) but are hidden from the default colorimetric output.

Texture Metrics (MeasureTexture)#

Haralick texture features computed from gray-level co-occurrence matrices at specified scales. These capture spatial patterns within colonies that size and shape metrics miss:

Smooth vs. rough colony surfaces
Concentric ring patterns
Internal structure differences between strains

Choosing Metrics#

Biological question	Metrics
Growth rate comparison	Area (time series)
Strain fitness ranking	Area + MeanIntensity
Morphology screening	Circularity + Solidity + Eccentricity
Pigmentation assay	MeanIntensity + CIELAB color channels
Colony heterogeneity	StandardDeviationIntensity + texture features