3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation
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We implemented comparison baselines (3D UNet, V-Net, Attention U-Net, nnFormer, UNETR) trained with the nnU-Net pipeline, and selected the finetuned VesselFM based on voxel Dice and instance Dice metrics from fivefold cross validation.
“As comparison baselines, we implemented the following architectures: 3D UNet57, V-Net51, Attention U-Net52, nnFormer53 and UNETR54. All were trained by using the nnU-Net pipeline56, with a patch size of 128 × 128 × 128 voxels, channel-wise z-score normalization, learning rate decay and SGD optimizer. The baselines were trained until convergence for 1,000 epochs and initial learning rates of [0.000”
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Bouget, D., Eijgelaar, R. S., Pedersen, A., Kommers, I., Ardon, H., Barkhof, F., Bello, L., Berger, M. S., Nibali, M. C., Furtner, J., et al. (2021) · Cancers · doi:10.3390/cancers13184674 · Cited by 19 · see citing works
Automatic Extraction of Hiatal Dimensions in 3-D Transperineal Pelvic Ultrasound Recordings
Williams, H., Cattani, L., Van Schoubroeck, D., Yaqub, M., Sudre, C., Vercauteren, T., D'Hooge, J., & Deprest, J. (2021) · Ultrasound in Medicine & Biology · doi:10.1016/j.ultrasmedbio.2021.08.009 · Cited by 19 · see citing works
clDice - a Novel Topology-Preserving Loss Function for Tubular Structure Segmentation
Shit, S., Paetzold, J. C., Sekuboyina, A., Ezhov, I., Unger, A., Zhylka, A., Pluim, J. P. W., Bauer, U., & Menze, B. H. (2021) · 2021 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR) · doi:10.1109/cvpr46437.2021.01629 · Cited by 60 · see citing works
“We trained two segmentation architectures, a U-Net and an FCN, for the various loss functions in our experimental setup.”
MethodJalalifar, S. A., Soliman, H., Sahgal, A., & Sadeghi-Naini, A. (2022) · Cancers · doi:10.3390/cancers14205133 · Cited by 15 · see citing works
Learning Interactive Real-World Simulators
Yang, S., Du, Y., Ghasemipour, K., Tompson, J., Kaelbling, L., Schuurmans, D., & Abbeel, P. (2023) · arXiv · doi:10.48550/arxiv.2310.06114 · Cited by 12 · see citing works
“We the 3D U-Net architecture [75, 28] to parametrize the UniSim video model.”
MethodA deep-learning framework reveals whole-body perturbations at cell level
Kaltenecker, D., Horvath, I., Al-Maskari, R., Chen, Y., Kolabas, Z. I., Hoeher, L., Todorov, M., Minde, D.-P., Kapoor, S., Turhan, S. G., et al. (2026) · Nature · doi:10.1038/s41586-026-10535-2 · Cited by 5 · see citing works
Video Diffusion Models: A Survey
Melnik, A., Ljubljanac, M., Lu, C., Yan, Q., Ren, W., & Ritter, H. (2024) · arXiv · doi:10.48550/arxiv.2405.03150 · Cited by 4 · see citing works
Wali, S., Khan, M. I., Samina, S., & Raza Sialvi, M. A. (2026) · 2026 11th International Conference on Image, Vision and Computing (ICIVC) · doi:10.1109/icivc70586.2026.11686729
- Authors
- Çiçek, Ö., Abdulkadir, A., Lienkamp, S. S., Brox, T., & Ronneberger, O.
- Affiliations
- University of Freiburg (DE)
- Corresponding author
- Çiçek, Özgün
- Venue
- Lecture Notes in Computer Science
- Publisher
- Springer International Publishing
- Published
- 2016
- Pages
- 424-432
- ISSN
- 0302-9743 (ISSN-L)
- 1611-3349
- OpenAlex
- W2464708700
- Cited by
- 7,945
- References
- 20
- Citations by year
- 2026: 666 · 2025: 1121 · 2024: 1165 · 2023: 1158 · 2022: 1063 · 2021: 1037 · 2020: 757 · 2019: 591 · 2018: 292 · 2017: 80 · 2016: 10 · 2015: 2 · 2012: 2
- FWCI
- 112.49
- Type
- conference paper
- Language
- en
- Open access
- green
- arxiv.org
- Locations
- Lecture notes in computer science (publishedVersion)
- arXiv (Cornell University) (submittedVersion)
- arXiv (Cornell University)
- Funders
- Deutsche Forschungsgemeinschaft (CRC1140, CRC1140_KIDGEM, (EXC 294))
- Topics
- Physical Sciences › Computer Science › Computer Vision and Pattern Recognition › Medical Image Segmentation Techniques
- Physical Sciences › Computer Science › Computer Vision and Pattern Recognition › Advanced Neural Network Applications
- Physical Sciences › Computer Science › Artificial Intelligence › Domain Adaptation and Few-Shot Learning
- Keywords
- 3D U-Net, 3D image segmentation, sparse annotations, semi-automatic segmentation, end-to-end learning, 3D medical image analysis
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