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Background  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.    Findings  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%    Conclusions  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.

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