Accurate Evaluation of HER-2 Amplification in FISH Images
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Accurate Evaluation of HER-2 Ampli cation in FISH Images Poster at International Conference on Imaging Systems and Techniques, Thessaloniki

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IEEE International Conference on Imaging Systems and Techniques, Thessaloniki, Greece / Poster

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Accurate Evaluation of HER-2 Ampli cation in FISH Images Poster at International Conference on Imaging Systems and Techniques, Thessaloniki

  1. 1. Accurate Evaluation of HER-2 Amplification in FISH Images A. 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 or absence of specific DNA sequences on chromosomes • A sample application of this technique targets the measurement of the amplification of the HER-2 gene within the 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 themselves to 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 within each nucleus • Inaccurate nuclei identification may severely bias the estimation of this ratio Adaptive threshold Input Image Distance transform for markers extraction Spot extraction Marked Watershed Reliability score Ratio evaluation A model for nuclei reliability Given a generic nucleus, its reliability score r is evaluated by The reliability score of a generic nucleus is evaluated as: measuring the compliance of the shape and size of the nucleus with respect to a template model. (a−at)2 (e−et)2 (c−ct)2 − 2 − 2 − 2 The reliability score of each nucleus is used so as to: r=e σa e σe e σc • Regions corresponding to a potentially oversegmented • a is the area of the nucleus and at the area of the template model nucleus are recursively merged so as to better match the • e is the eccentricity of the nucleus and et the eccentricity of the template model actual shape and contour of the nucleus • c is the convexity of the nucleus and ct the convexity of the template model • Nuclei can be ordered by decreasing reliability scores so as to Values of σa, σe and σc define the range of allowable deviations from template area and compute the ratio of HER-2 over CEP-17 markers using only eccentricity. Values of parameters at, et and ct have been estimated by averaging the actual values the most reliable ones measured on a training dataset. The Dataset Results The dataset consists of 40 FISH images extracted from eight 0,9 Classification accuracy is slides of breast tissue samples. Each image is annotated by an measured through the expert pathologist with a classification label corresponding to four 0,8 confusion matrix and is different levels of HER-2 amplification: evaluated for the test dataset • No amplification (N), 17.5% of the dataset 0,7 using the optimal value of τr • Borderline (B), 10.0% 0,6 identified on the training • Amplified (A), 25.0% dataset. • Strong amplification (A+), 47.5% 0,5 N B A A+ The system automatically classifies a generic image based on the 0,4 N 1.0 0.0 0.0 0.0 average value ρ of the ratio extracted on nuclei with a reliability B 0.0 1.0 0.0 0.0 score r higher than a threshold τr . 0,3 A 0.0 0.0 0.875 0.125 The optimal value of τr is computed by maximizing classification 0 0,1 0,2 0,3 0,4 0,5 0,6 0,7 0,8 0,9 A+ 0.0 0.0 0.125 0.875 accuracy over a training dataset. http://www.dsi.unifi.it/pala/ http://www.micc.unifi.it/projects/her-2/ {delbimbo,meoni,pala}@dsi.unifi.it

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