no code implementations • 23 Dec 2024 • Junyu Chen, Shuwen Wei, Yihao Liu, Zhangxing Bian, Yufan He, Aaron Carass, Harrison Bai, Yong Du
Spatially varying regularization accommodates the deformation variations that may be necessary for different anatomical regions during deformable image registration.
no code implementations • 19 Nov 2024 • Vishwesh Nath, Wenqi Li, Dong Yang, Andriy Myronenko, Mingxin Zheng, Yao Lu, Zhijian Liu, Hongxu Yin, Yee Man Law, Yucheng Tang, Pengfei Guo, Can Zhao, Ziyue Xu, Yufan He, Greg Heinrich, Stephen Aylward, Marc Edgar, Michael Zephyr, Pavlo Molchanov, Baris Turkbey, Holger Roth, Daguang Xu
In contrast, we propose that for medical VLMs, a fourth stage of specialized IFT is necessary, which focuses on medical data and includes information from domain expert models.
1 code implementation • 20 Aug 2024 • Yufan He, Pengfei Guo, Yucheng Tang, Andriy Myronenko, Vishwesh Nath, Ziyue Xu, Dong Yang, Can Zhao, Daguang Xu, Wenqi Li
Since the release of Segment Anything 2 (SAM2), the medical imaging community has been actively evaluating its performance for 3D medical image segmentation.
no code implementations • 3 Jul 2024 • Yucheng Tang, Yufan He, Vishwesh Nath, Pengfeig Guo, Ruining Deng, Tianyuan Yao, Quan Liu, Can Cui, Mengmeng Yin, Ziyue Xu, Holger Roth, Daguang Xu, Haichun Yang, Yuankai Huo
In this paper, we propose the holistic histopathology (HoloHisto) segmentation method to achieve end-to-end segmentation on gigapixel WSIs, whose maximum resolution is above 80, 000$\times$70, 000 pixels.
1 code implementation • 7 Jun 2024 • Yufan He, Pengfei Guo, Yucheng Tang, Andriy Myronenko, Vishwesh Nath, Ziyue Xu, Dong Yang, Can Zhao, Benjamin Simon, Mason Belue, Stephanie Harmon, Baris Turkbey, Daguang Xu, Wenqi Li
The novel model design and training recipe represent a promising step toward developing a versatile medical image foundation model and will serve as a valuable foundation for CT image analysis.
1 code implementation • 6 Oct 2023 • Andriy Myronenko, Dong Yang, Yufan He, Daguang Xu
Kidney and Kidney Tumor Segmentation Challenge (KiTS) 2023 offers a platform for researchers to compare their solutions to segmentation from 3D CT.
1 code implementation • 6 Oct 2023 • Andriy Myronenko, Dong Yang, Yufan He, Daguang Xu
In this work, we describe our solution to the Segmentation of the Aorta (SEG. A. 231) from 3D CT challenge.
1 code implementation • 31 Jul 2023 • Jeya Maria Jose Valanarasu, Yucheng Tang, Dong Yang, Ziyue Xu, Can Zhao, Wenqi Li, Vishal M. Patel, Bennett Landman, Daguang Xu, Yufan He, Vishwesh Nath
We curate a large-scale dataset to enable pre-training of 3D medical radiology images (MRI and CT).
no code implementations • 10 Mar 2023 • Junyu Chen, Yihao Liu, Yufan He, Yong Du
Transformers have recently shown promise for medical image applications, leading to an increasing interest in developing such models for medical image registration.
no code implementations • 10 Mar 2023 • Junyu Chen, Yihao Liu, Yufan He, Yong Du
In the past, optimization-based registration models have used spatially-varying regularization to account for deformation variations in different image regions.
2 code implementations • 4 Nov 2022 • M. Jorge Cardoso, Wenqi Li, Richard Brown, Nic Ma, Eric Kerfoot, Yiheng Wang, Benjamin Murrey, Can Zhao, Dong Yang, Vishwesh Nath, Yufan He, Ziyue Xu, Ali Hatamizadeh, Andriy Myronenko, Wentao Zhu, Yun Liu, Mingxin Zheng, Yucheng Tang, Isaac Yang, Michael Zephyr, Behrooz Hashemian, Sachidanand Alle, Mohammad Zalbagi Darestani, Charlie Budd, Marc Modat, Tom Vercauteren, Guotai Wang, Yiwen Li, Yipeng Hu, Yunguan Fu, Benjamin Gorman, Hans Johnson, Brad Genereaux, Barbaros S. Erdal, Vikash Gupta, Andres Diaz-Pinto, Andre Dourson, Lena Maier-Hein, Paul F. Jaeger, Michael Baumgartner, Jayashree Kalpathy-Cramer, Mona Flores, Justin Kirby, Lee A. D. Cooper, Holger R. Roth, Daguang Xu, David Bericat, Ralf Floca, S. Kevin Zhou, Haris Shuaib, Keyvan Farahani, Klaus H. Maier-Hein, Stephen Aylward, Prerna Dogra, Sebastien Ourselin, Andrew Feng
For AI models to be used clinically, they need to be made safe, reproducible and robust, and the underlying software framework must be aware of the particularities (e. g. geometry, physiology, physics) of medical data being processed.
1 code implementation • 22 Sep 2022 • Andriy Myronenko, Md Mahfuzur Rahman Siddiquee, Dong Yang, Yufan He, Daguang Xu
Head and neck tumor segmentation challenge (HECKTOR) 2022 offers a platform for researchers to compare their solutions to segmentation of tumors and lymph nodes from 3D CT and PET images.
no code implementations • 21 Sep 2022 • Md Mahfuzur Rahman Siddiquee, Dong Yang, Yufan He, Daguang Xu, Andriy Myronenko
Intracranial hemorrhage segmentation challenge (INSTANCE 2022) offers a platform for researchers to compare their solutions to segmentation of hemorrhage stroke regions from 3D CTs.
no code implementations • 20 Sep 2022 • Md Mahfuzur Rahman Siddique, Dong Yang, Yufan He, Daguang Xu, Andriy Myronenko
Ischemic Stroke Lesion Segmentation challenge (ISLES 2022) offers a platform for researchers to compare their solutions to 3D segmentation of ischemic stroke regions from 3D MRIs.
no code implementations • CVPR 2022 • Cheng Peng, Andriy Myronenko, Ali Hatamizadeh, Vish Nath, Md Mahfuzur Rahman Siddiquee, Yufan He, Daguang Xu, Rama Chellappa, Dong Yang
Given the recent success of deep learning in medical image segmentation, Neural Architecture Search (NAS) has been introduced to find high-performance 3D segmentation network architectures.
1 code implementation • 19 Nov 2021 • Junyu Chen, Eric C. Frey, Yufan He, William P. Segars, Ye Li, Yong Du
Recently Vision Transformer architectures have been proposed to address the shortcomings of ConvNets and have produced state-of-the-art performances in many medical imaging applications.
Ranked #1 on
Medical Image Registration
on OASIS
1 code implementation • 13 Apr 2021 • Junyu Chen, Yufan He, Eric C. Frey, Ye Li, Yong Du
However, the performances of ConvNets are still limited by lacking the understanding of long-range spatial relations in an image.
Ranked #4 on
Medical Image Registration
on OASIS
1 code implementation • CVPR 2021 • Yufan He, Dong Yang, Holger Roth, Can Zhao, Daguang Xu
In this work, we focus on three important aspects of NAS in 3D medical image segmentation: flexible multi-path network topology, high search efficiency, and budgeted GPU memory usage.
no code implementations • 24 Mar 2021 • Lianrui Zuo, Blake E. Dewey, Aaron Carass, Yihao Liu, Yufan He, Peter A. Calabresi, Jerry L. Prince
Accuracy and consistency are two key factors in computer-assisted magnetic resonance (MR) image analysis.
1 code implementation • 7 Jul 2020 • Yufan He, Aaron Carass, Lianrui Zuo, Blake E. Dewey, Jerry L. Prince
However, training a model for each target domain is time consuming and computationally expensive, even infeasible when target domain data are scarce or source data are unavailable due to data privacy.
2 code implementations • 11 Feb 2020 • Jacob C. Reinhold, Yufan He, Shizhong Han, Yunqiang Chen, Dashan Gao, Junghoon Lee, Jerry L. Prince, Aaron Carass
Medical images are often used to detect and characterize pathology and disease; however, automatically identifying and segmenting pathology in medical images is challenging because the appearance of pathology across diseases varies widely.
1 code implementation • 11 Feb 2020 • Jacob C. Reinhold, Yufan He, Shizhong Han, Yunqiang Chen, Dashan Gao, Junghoon Lee, Jerry L. Prince, Aaron Carass
Medical images are increasingly used as input to deep neural networks to produce quantitative values that aid researchers and clinicians.
no code implementations • 14 Mar 2018 • Yufan He, Aaron Carass, Bruno M. Jedynak, Sharon D. Solomon, Shiv Saidha, Peter A. Calabresi, Jerry L. Prince
Optical coherence tomography (OCT) is a noninvasive imaging modality which can be used to obtain depth images of the retina.
no code implementations • 5 Aug 2015 • Yankui Sun, Tian Zhang, Yue Zhao, Yufan He
We present here a novel 3D automatic segmentation method for retinal OCT volume data.