OCTID: a one-class learning-based Python package for tumor image detection.

Abstract

Tumor tile selection is a necessary prerequisite in patch-based cancer whole slide image analysis, which is labor-intensive and requires expertise. Whole slides are annotated as tumor or tumor free, but tiles within a tumor slide are not. As all tiles within a tumor free slide are tumor free, these can be used to capture tumor-free patterns using the one-class learning strategy. We present a Python package, termed OCTID, which combines a pretrained convolutional neural network (CNN) model, Uniform Manifold Approximation and Projection (UMAP) and one-class support vector machine to achieve accurate tumor tile classification using a training set of tumor free tiles. Benchmarking experiments on four H&E image datasets achieved remarkable performance in terms of F1-score (0.90 ± 0.06), Matthews correlation coefficient (0.93 ± 0.05) and accuracy (0.94 ± 0.03). Detailed information can be found in the Supplementary File. Supplementary data are available at Bioinformatics online.