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.

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 use the CIELAB, HSV, and CIE XYZ color spaces. Key columns include mean, median, and standard deviation for each channel. These are essential for:

• Quantifying pigmentation differences between strains

• Detecting sectoring (regions of different color within a colony)

• Normalizing color across imaging sessions (after ColorCorrector)

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