How to select slices for annotation to train best-performing deep learning segmentation models for cross-sectional medical images?

Yixin Zhang, Kevin Kramer, Maciej A Mazurowski
Proceedings of The 8th International Conference on Medical Imaging with Deep Learning, PMLR 301:1811-1831, 2026.

Abstract

Automated segmentation of medical images heavily relies on the availability of precise manual annotations. However, generating these annotations is often time-consuming, expensive, and sometimes requires specialized expertise (especially for cross-sectional medical images). Therefore, it is essential to optimize the use of annotation resources to ensure efficiency and effectiveness. In this paper, we systematically address the question: ïn a non-interactive annotation pipeline, how should slices from cross-sectional medical images be selected for annotation to maximize the performance of the resulting deep learning segmentation models?Ẅe conducted experiments on 4 medical imaging segmentation tasks with varying annotation budgets, numbers of annotated cases, numbers of annotated slices per volume, slice selection techniques, and mask interpolations. We found that:1) It is almost always preferable to annotate fewer slices per volume and more volumes given an annotation budget. 2) Selecting slices for annotation by unsupervised active learning (UAL) is not superior to selecting slices randomly or at fixed intervals, provided that each volume is allocated the same number of annotated slices. 3) Interpolating masks between annotated slices rarely enhances model performance, with exceptions of some specific configuration for 3D models.

Cite this Paper

BibTeX
@InProceedings{pmlr-v301-zhang26a, title = {How to select slices for annotation to train best-performing deep learning segmentation models for cross-sectional medical images?}, author = {Zhang, Yixin and Kramer, Kevin and Mazurowski, Maciej A}, booktitle = {Proceedings of The 8th International Conference on Medical Imaging with Deep Learning}, pages = {1811--1831}, year = {2026}, editor = {Tasdizen, Tolga and Elhabian, Shireen and Summers, Ronald and Chen, Chen and Koch, Lisa and Zhuang, Yan}, volume = {301}, series = {Proceedings of Machine Learning Research}, month = {09--11 Jul}, publisher = {PMLR}, pdf = {https://raw.githubusercontent.com/mlresearch/v301/main/assets/zhang26a/zhang26a.pdf}, url = {https://proceedings.mlr.press/v301/zhang26a.html}, abstract = {Automated segmentation of medical images heavily relies on the availability of precise manual annotations. However, generating these annotations is often time-consuming, expensive, and sometimes requires specialized expertise (especially for cross-sectional medical images). Therefore, it is essential to optimize the use of annotation resources to ensure efficiency and effectiveness. In this paper, we systematically address the question: ïn a non-interactive annotation pipeline, how should slices from cross-sectional medical images be selected for annotation to maximize the performance of the resulting deep learning segmentation models?Ẅe conducted experiments on 4 medical imaging segmentation tasks with varying annotation budgets, numbers of annotated cases, numbers of annotated slices per volume, slice selection techniques, and mask interpolations. We found that:1) It is almost always preferable to annotate fewer slices per volume and more volumes given an annotation budget. 2) Selecting slices for annotation by unsupervised active learning (UAL) is not superior to selecting slices randomly or at fixed intervals, provided that each volume is allocated the same number of annotated slices. 3) Interpolating masks between annotated slices rarely enhances model performance, with exceptions of some specific configuration for 3D models.} }
Endnote
%0 Conference Paper %T How to select slices for annotation to train best-performing deep learning segmentation models for cross-sectional medical images? %A Yixin Zhang %A Kevin Kramer %A Maciej A Mazurowski %B Proceedings of The 8th International Conference on Medical Imaging with Deep Learning %C Proceedings of Machine Learning Research %D 2026 %E Tolga Tasdizen %E Shireen Elhabian %E Ronald Summers %E Chen Chen %E Lisa Koch %E Yan Zhuang %F pmlr-v301-zhang26a %I PMLR %P 1811--1831 %U https://proceedings.mlr.press/v301/zhang26a.html %V 301 %X Automated segmentation of medical images heavily relies on the availability of precise manual annotations. However, generating these annotations is often time-consuming, expensive, and sometimes requires specialized expertise (especially for cross-sectional medical images). Therefore, it is essential to optimize the use of annotation resources to ensure efficiency and effectiveness. In this paper, we systematically address the question: ïn a non-interactive annotation pipeline, how should slices from cross-sectional medical images be selected for annotation to maximize the performance of the resulting deep learning segmentation models?Ẅe conducted experiments on 4 medical imaging segmentation tasks with varying annotation budgets, numbers of annotated cases, numbers of annotated slices per volume, slice selection techniques, and mask interpolations. We found that:1) It is almost always preferable to annotate fewer slices per volume and more volumes given an annotation budget. 2) Selecting slices for annotation by unsupervised active learning (UAL) is not superior to selecting slices randomly or at fixed intervals, provided that each volume is allocated the same number of annotated slices. 3) Interpolating masks between annotated slices rarely enhances model performance, with exceptions of some specific configuration for 3D models.
APA
Zhang, Y., Kramer, K. & Mazurowski, M.A.. (2026). How to select slices for annotation to train best-performing deep learning segmentation models for cross-sectional medical images?. Proceedings of The 8th International Conference on Medical Imaging with Deep Learning, in Proceedings of Machine Learning Research 301:1811-1831 Available from https://proceedings.mlr.press/v301/zhang26a.html.

Related Material