How To: Measure Colony Size and Intensity

Extract area, perimeter, circularity, and intensity statistics from detected colonies using MeasureSize, MeasureShape, and MeasureIntensity.

import phenotypic as pht
from phenotypic.data import load_yeast_plate
from phenotypic.enhance import GaussianBlur, EnhanceLocalContrast
from phenotypic.detect import OtsuDetector
from phenotypic.measure import MeasureSize, MeasureShape, MeasureIntensity

pipeline = pht.ImagePipeline(
    ops=[GaussianBlur(sigma=2.0), EnhanceLocalContrast(clip_limit=0.01), OtsuDetector()],
    meas=[MeasureSize(), MeasureShape(), MeasureIntensity()],
)
df = pipeline.apply_and_measure(load_yeast_plate())

Size Metrics

df[["Size_Area", "Size_IntegratedIntensity"]].describe()

	Size_Area	Size_IntegratedIntensity
count	7.000000	7.000000
mean	16869.857143	9842.796991
std	3076.517210	1929.831898
min	13329.000000	7522.484134
25%	14984.500000	8566.098591
50%	17055.000000	9998.177169
75%	17533.000000	10501.255212
max	22670.000000	13244.210029

Shape Metrics

df[["Shape_Circularity", "Shape_Solidity", "Shape_Eccentricity"]].describe()

	Shape_Circularity	Shape_Solidity	Shape_Eccentricity
count	7.000000	7.000000	7.000000
mean	0.894006	36.400345	0.276039
std	0.010850	3.194938	0.041446
min	0.879643	32.498452	0.207857
25%	0.885698	34.510547	0.261318
50%	0.897971	36.520339	0.279115
75%	0.900684	37.271280	0.290936
max	0.907665	42.219969	0.340791

Intensity Metrics

df[["Intensity_MeanIntensity", "Intensity_MedianIntensity", "Intensity_StandardDeviationIntensity"]].describe()

	Intensity_MeanIntensity	Intensity_MedianIntensity	Intensity_StandardDeviationIntensity
count	7.000000	7.000000	7.000000
mean	0.582158	0.591675	0.041818
std	0.015325	0.016415	0.003861
min	0.564370	0.574488	0.037359
25%	0.571459	0.579269	0.038207
50%	0.583767	0.591588	0.042502
75%	0.586948	0.597608	0.045163
max	0.610154	0.621897	0.046125

The DataFrame has one row per colony. Filter, sort, and group using standard pandas operations to answer biological questions.