Accurate Evaluation of HER-2 Amplification in FISH ImagesA. Del Bimbo, M. Meoni, P. Pala

Dipartimento Sistemi e Informatica, University of Firenze, Italy

Context and motivations

• Fluorescence in situ hybridization (FISH) is a cytogenetic technique used to detect and localize the presence orabsence of specific DNA sequences on chromosomes

• A sample application of this technique targets the measurement of the amplification of the HER-2 gene withinthe chromosomes, that constitutes a valuable indicator of invasive breast carcinomas

• This requires the application to a tumor tissue sample of two types of fluorescent probes that attach themselvesto the HER-2 genes and to the centromere 17 (CEP-17), respectively

• Estimation of HER-2 amplification is accomplished by measuring the ratio of HER-2 over CEP-17 markers withineach nucleus

• Inaccurate nuclei identification may severely bias the estimation of this ratio

Distance transform for markers extraction

Adaptive threshold

Ratio evaluation

Input Image

Spot extraction

Marked Watershed

Reliability score

A model for nuclei reliability

Given a generic nucleus, its reliability score r is evaluated bymeasuring the compliance of the shape and size of the nucleuswith respect to a template model.

The reliability score of each nucleus is used so as to:

• Regions corresponding to a potentially oversegmentednucleus are recursively merged so as to better match theactual shape and contour of the nucleus

• Nuclei can be ordered by decreasing reliability scores so as tocompute the ratio of HER-2 over CEP-17 markers using onlythe most reliable ones

The reliability score of a generic nucleus is evaluated as:

r = e−(a−at)2

σ2a e−(e−et)2

σ2e e−(c−ct)2

σ2c

• a is the area of the nucleus and at the area of the template model

• e is the eccentricity of the nucleus and et the eccentricity of the template model

• c is the convexity of the nucleus and ct the convexity of the template model

Values of σa, σe and σc define the range of allowable deviations from template area andeccentricity. Values of parameters at, et and ct have been estimated by averaging the actual valuesmeasured on a training dataset.

The Dataset

The dataset consists of 40 FISH images extracted from eightslides of breast tissue samples. Each image is annotated by anexpert pathologist with a classification label corresponding to fourdifferent levels of HER-2 amplification:

• No amplification (N), 17.5% of the dataset

• Borderline (B), 10.0%

• Amplified (A), 25.0%

• Strong amplification (A+), 47.5%

The system automatically classifies a generic image based on theaverage value ρ of the ratio extracted on nuclei with a reliabilityscore r higher than a threshold τr.The optimal value of τr is computed by maximizing classificationaccuracy over a training dataset.

Results

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0 0,1 0,2 0,3 0,4 0,5 0,6 0,7 0,8 0,9

Classification accuracy ismeasured through theconfusion matrix and isevaluated for the test datasetusing the optimal value of τridentified on the trainingdataset.

N B A A+N 1.0 0.0 0.0 0.0B 0.0 1.0 0.0 0.0A 0.0 0.0 0.875 0.125A+ 0.0 0.0 0.125 0.875

http://www.dsi.unifi.it/pala/ http://www.micc.unifi.it/projects/her-2/ {delbimbo,meoni,pala}@dsi.unifi.it