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Open Access Technical Note

Performance of a simple chromatin-rich segmentation algorithm in quantifying basal cell carcinoma from histology images

Kyle Lesack1 and Christopher Naugler2*

Author Affiliations

1 Room G503, O'Brien Centre for the BHSc, 3330 Hospital Drive N.W., Calgary, Alberta T2N 4N1, Canada

2 Department of Pathology and Laboratory Medicine, University of Calgary and Calgary Laboratory Services, C414, Diagnostic and Scientific Centre 9, 3535 Research Road NW, Calgary, AB T2L 2 K8, Canada

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BMC Research Notes 2012, 5:35  doi:10.1186/1756-0500-5-35

Published: 17 January 2012



The use of digital imaging and algorithm-assisted identification of regions of interest is revolutionizing the practice of anatomic pathology. Currently automated methods for extracting the tumour regions in basal cell carcinomas are lacking. In this manuscript a colour-deconvolution based tumour extraction algorithm is presented.


Haematoxylin and eosin stained basal cell carcinoma histology slides were digitized and analyzed using the open source image analysis program ImageJ. The pixels belonging to tumours were identified by the algorithm, and the performance of the algorithm was evaluated by comparing the pixels identified as malignant with a manually determined dataset.

The algorithm achieved superior results with the nodular tumour subtype. Pre-processing using colour deconvolution resulted in a slight decrease in sensitivity, but a significant increase in specificity. The overall sensitivity and specificity of the algorithm was 91.0% and 86.4% respectively, resulting in a positive predictive value of 63.3% and a negative predictive value of 94.2%


The proposed image analysis algorithm demonstrates the feasibility of automatically extracting tumour regions from digitized basal cell carcinoma histology slides. The proposed algorithm may be adaptable to other stain combinations and tumour types.