Dataset creation for supervised deep learning-based analysis of microscopic images -- review of important considerations and recommendations

Christof A. Bertram; Viktoria Weiss; Jonas Ammeling; F. Maria Schabel; Taryn A. Donovan; Frauke Wilm; Christian Marzahl; Katharina Breininger; Marc Aubreville

arXiv · 2512.04564

Dataset creation for supervised deep learning-based analysis of microscopic images -- review of important considerations and recommendations

Christof A. Bertram·Viktoria Weiss·Jonas Ammeling·F. Maria Schabel·Taryn A. Donovan·Frauke Wilm·Christian Marzahl·Katharina Breininger·Marc Aubreville

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Abstract

Supervised deep learning (DL) receives great interest for automated analysis of microscopic images with an increasing body of literature supporting its potential. The development and validation of those DL models relies heavily on the availability of high-quality, large-scale datasets. However, creating such datasets is a complex and resource-intensive process, often hindered by challenges such as time constraints, domain variability, and risks of bias in image collection and label creation. This review provides a comprehensive guide to the critical steps in dataset creation, including: 1) image acquisition, 2) selection of annotation software, and 3) annotation creation. In addition to ensuring a sufficiently large number of images, it is crucial to address sources of image variability (domain shifts) - such as those related to slide preparation and digitization - that could lead to algorithmic errors if not adequately represented in the training data. Key quality criteria for annotations are the three "C"s: correctness, completeness, and consistency. This review explores methods to enhance annotation quality through the use of advanced techniques that mitigate the limitations of single annotators. To support dataset creators, a standard operating procedure (SOP) is provided as supplemental material, outlining best practices for dataset development. Furthermore, the article underscores the importance of open datasets in driving innovation and enhancing reproducibility of DL research. By addressing the challenges and offering practical recommendations, this review aims to advance the creation of and availability to high-quality, large-scale datasets, ultimately contributing to the development of generalizable and robust DL models for pathology applications.

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BibTeX RIS

Christof A. Bertram, Viktoria Weiss, Jonas Ammeling, F. Maria Schabel, Taryn A. Donovan, Frauke Wilm, Christian Marzahl, Katharina Breininger, Marc Aubreville. 2025-12-04. Dataset creation for supervised deep learning-based analysis of microscopic images -- review of important considerations and recommendations. https://arxiv.org/abs/2512.04564

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