no code implementations • 29 Feb 2024 • Ruining Deng, Quan Liu, Can Cui, Tianyuan Yao, Jialin Yue, Juming Xiong, Lining Yu, Yifei Wu, Mengmeng Yin, Yu Wang, Shilin Zhao, Yucheng Tang, Haichun Yang, Yuankai Huo
Understanding the anatomy of renal pathology is crucial for advancing disease diagnostics, treatment evaluation, and clinical research.
1 code implementation • 10 Aug 2023 • Jiayuan Chen, Yu Wang, Ruining Deng, Quan Liu, Can Cui, Tianyuan Yao, Yilin Liu, Jianyong Zhong, Agnes B. Fogo, Haichun Yang, Shilin Zhao, Yuankai Huo
Podocytes, specialized epithelial cells that envelop the glomerular capillaries, play a pivotal role in maintaining renal health.
no code implementations • 1 Jul 2023 • Can Cui, Ruining Deng, Quan Liu, Tianyuan Yao, Shunxing Bao, Lucas W. Remedios, Yucheng Tang, Yuankai Huo
The Segment Anything Model (SAM) is a recently proposed prompt-based segmentation model in a generic zero-shot segmentation approach.
no code implementations • 5 Jun 2023 • Tianyuan Yao, Francois Rheault, Leon Y Cai, Vishwesh Nath, Zuhayr Asad, Nancy Newlin, Can Cui, Ruining Deng, Karthik Ramadass, Andrea Shafer, Susan Resnick, Kurt Schilling, Bennett A. Landman, Yuankai Huo
From the experimental results, the proposed data-driven framework outperforms the existing benchmarks in repeated fODF estimation.
no code implementations • 9 Apr 2023 • Ruining Deng, Can Cui, Quan Liu, Tianyuan Yao, Lucas W. Remedios, Shunxing Bao, Bennett A. Landman, Lee E. Wheless, Lori A. Coburn, Keith T. Wilson, Yaohong Wang, Shilin Zhao, Agnes B. Fogo, Haichun Yang, Yucheng Tang, Yuankai Huo
However, it does not consistently achieve satisfying performance for dense instance object segmentation, even with 20 prompts (clicks/boxes) on each image.
no code implementations • 29 Mar 2023 • Tianyuan Yao, Nancy Newlin, Praitayini Kanakaraj, Vishwesh Nath, Leon Y Cai, Karthik Ramadass, Kurt Schilling, Bennett A. Landman, Yuankai Huo
Diffusion-weighted (DW) MRI measures the direction and scale of the local diffusion process in every voxel through its spectrum in q-space, typically acquired in one or more shells.
1 code implementation • 30 Aug 2022 • Tianyuan Yao, Chang Qu, Jun Long, Quan Liu, Ruining Deng, Yuanhan Tian, Jiachen Xu, Aadarsh Jha, Zuhayr Asad, Shunxing Bao, Mengyang Zhao, Agnes B. Fogo, Bennett A. Landman, Haichun Yang, Catie Chang, Yuankai Huo
In order to extract and separate compound figures into usable individual images for downstream learning, we propose a simple compound figure separation (SimCFS) framework without using the traditionally required detection bounding box annotations, with a new loss function and a hard case simulation.
1 code implementation • 27 Jun 2022 • Ruining Deng, Quan Liu, Can Cui, Tianyuan Yao, Jun Long, Zuhayr Asad, R. Michael Womick, Zheyu Zhu, Agnes B. Fogo, Shilin Zhao, Haichun Yang, Yuankai Huo
The contribution of this paper is three-fold: (1) a novel scale-aware controller is proposed to generalize the dynamic neural network from single-scale to multi-scale; (2) semi-supervised consistency regularization of pseudo-labels is introduced to model the inter-scale correlation of unannotated tissue types into a single end-to-end learning paradigm; and (3) superior scale-aware generalization is evidenced by directly applying a model trained on human kidney images to mouse kidney images, without retraining.
1 code implementation • 31 May 2022 • Tianyuan Yao, Yuzhe Lu, Jun Long, Aadarsh Jha, Zheyu Zhu, Zuhayr Asad, Haichun Yang, Agnes B. Fogo, Yuankai Huo
To leverage the performance of the Glo-In-One toolkit, we introduce self-supervised deep learning to glomerular quantification via large-scale web image mining.
1 code implementation • 31 Jan 2022 • Yuzhe Lu, Haichun Yang, Zuhayr Asad, Zheyu Zhu, Tianyuan Yao, Jiachen Xu, Agnes B. Fogo, Yuankai Huo
Recent studies have demonstrated the diagnostic and prognostic values of global glomerulosclerosis (GGS) in IgA nephropathy, aging, and end-stage renal disease.
1 code implementation • 19 Jul 2021 • Tianyuan Yao, Chang Qu, Quan Liu, Ruining Deng, Yuanhan Tian, Jiachen Xu, Aadarsh Jha, Shunxing Bao, Mengyang Zhao, Agnes B. Fogo, Bennett A. Landman, Catie Chang, Haichun Yang, Yuankai Huo
Our technical contribution is three-fold: (1) we introduce a new side loss that is designed for compound figure separation; (2) we introduce an intra-class image augmentation method to simulate hard cases; (3) the proposed framework enables an efficient deployment to new classes of images, without requiring resource extensive bounding box annotations.
no code implementations • 22 Jun 2021 • Mengyang Zhao, Quan Liu, Aadarsh Jha, Ruining Deng, Tianyuan Yao, Anita Mahadevan-Jansen, Matthew J. Tyska, Bryan A. Millis, Yuankai Huo
Recently, pixel embedding-based cell instance segmentation and tracking provided a neat and generalizable computing paradigm for understanding cellular dynamics.
1 code implementation • 9 Mar 2021 • Quan Liu, Peter C. Louis, Yuzhe Lu, Aadarsh Jha, Mengyang Zhao, Ruining Deng, Tianyuan Yao, Joseph T. Roland, Haichun Yang, Shilin Zhao, Lee E. Wheless, Yuankai Huo
The contribution of the paper is three-fold: (1) The proposed SimTriplet method takes advantage of the multi-view nature of medical images beyond self-augmentation; (2) The method maximizes both intra-sample and inter-sample similarities via triplets from positive pairs, without using negative samples; and (3) The recent mix precision training is employed to advance the training by only using a single GPU with 16GB memory.