SELMA3D challenge: Self-supervised learning for 3D light-sheet microscopy image segmentation

Ying Chen; Rami Al-Maskari; Izabela Horvath; Mayar Ali; Luciano Hoher; Kaiyuan Yang; Zengming Lin; Zhiwei Zhai; Mengzhe Shen; Dejin Xun; Yi Wang; Tony Xu; Maged Goubran; Yunheng Wu; Kensaku Mori; Johannes C. Paetzold; Ali Erturk

arXiv · 2501.03880

SELMA3D challenge: Self-supervised learning for 3D light-sheet microscopy image segmentation

Ying Chen·Rami Al-Maskari·Izabela Horvath·Mayar Ali·Luciano Hoher·Kaiyuan Yang·Zengming Lin·Zhiwei Zhai·Mengzhe Shen·Dejin Xun·Yi Wang·Tony Xu·Maged Goubran·Yunheng Wu·Kensaku Mori·Johannes C. Paetzold·Ali Erturk

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Abstract

Recent innovations in light sheet microscopy, paired with developments in tissue clearing techniques, enable the 3D imaging of large mammalian tissues with cellular resolution. Combined with the progress in large-scale data analysis, driven by deep learning, these innovations empower researchers to rapidly investigate the morphological and functional properties of diverse biological samples. Segmentation, a crucial preliminary step in the analysis process, can be automated using domain-specific deep learning models with expert-level performance. However, these models exhibit high sensitivity to domain shifts, leading to a significant drop in accuracy when applied to data outside their training distribution. To address this limitation, and inspired by the recent success of self-supervised learning in training generalizable models, we organized the SELMA3D Challenge during the MICCAI 2024 conference. SELMA3D provides a vast collection of light-sheet images from cleared mice and human brains, comprising 35 large 3D images-each with over 1000^3 voxels-and 315 annotated small patches for finetuning, preliminary testing and final testing. The dataset encompasses diverse biological structures, including vessel-like and spot-like structures. Five teams participated in all phases of the challenge, and their proposed methods are reviewed in this paper. Quantitative and qualitative results from most participating teams demonstrate that self-supervised learning on large datasets improves segmentation model performance and generalization. We will continue to support and extend SELMA3D as an inaugural MICCAI challenge focused on self-supervised learning for 3D microscopy image segmentation.

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Ying Chen, Rami Al-Maskari, Izabela Horvath, Mayar Ali, Luciano Hoher, Kaiyuan Yang, Zengming Lin, Zhiwei Zhai, Mengzhe Shen, Dejin Xun, Yi Wang, Tony Xu, Maged Goubran, Yunheng Wu, Kensaku Mori, Johannes C. Paetzold, Ali Erturk. 2025-01-07. SELMA3D challenge: Self-supervised learning for 3D light-sheet microscopy image segmentation. https://arxiv.org/abs/2501.03880

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