Daniela P. Schacherer

Daniela P. Schacherer, Markus D. Herrmann, David A. Clunie et al.

Background and Objectives: Reproducibility is a major challenge in developing machine learning (ML)-based solutions in computational pathology (CompPath). The NCI Imaging Data Commons (IDC) provides >120 cancer image collections according to the FAIR principles and is designed to be used with cloud ML services. Here, we explore its potential to facilitate reproducibility in CompPath research. Methods: Using the IDC, we implemented two experiments in which a representative ML-based method for classifying lung tumor tissue was trained and/or evaluated on different datasets. To assess reproducibility, the experiments were run multiple times with separate but identically configured instances of common ML services. Results: The AUC values of different runs of the same experiment were generally consistent. However, we observed small variations in AUC values of up to 0.045, indicating a practical limit to reproducibility. Conclusions: We conclude that the IDC facilitates approaching the reproducibility limit of CompPath research (i) by enabling researchers to reuse exactly the same datasets and (ii) by integrating with cloud ML services so that experiments can be run in identically configured computing environments.

Henning Höfener, Farina Kock, Martina Pontones et al.

Leukemia diagnosis primarily relies on manual microscopic analysis of bone marrow morphology supported by additional laboratory parameters, making it complex and time consuming. While artificial intelligence (AI) solutions have been proposed, most utilize private datasets and only cover parts of the diagnostic pipeline. Therefore, we present a large, high-quality, publicly available leukemia bone marrow dataset spanning the entire diagnostic process, from cell detection to diagnosis. Using this dataset, we further propose methods for cell detection, cell classification, and diagnosis prediction. The dataset comprises 246 pediatric patients with diagnostic, clinical and laboratory information, over 40 000 cells with bounding box annotations and more than 28 000 of these with high-quality class labels, making it the most comprehensive dataset publicly available. Evaluation of the AI models yielded an average precision of 0.96 for the cell detection, an area under the curve of 0.98, and an F1-score of 0.61 for the 33-class cell classification, and a mean F1-score of 0.90 for the diagnosis prediction using predicted cell counts. While the proposed approaches demonstrate their usefulness for AI-assisted diagnostics, the dataset will foster further research and development in the field, ultimately contributing to more precise diagnoses and improved patient outcomes.