no code implementations • 1 Feb 2023 • Ruida Zeng, Aadarsh Jha, Ashwin Kumar, Terry Luo
Herein, we present Stratus, an end-to-end full-stack deep learning application deployed on the cloud.
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 • 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 • 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.
no code implementations • 4 Mar 2021 • Yuzhe Lu, Aadarsh Jha, Yuankai Huo
In this paper, we investigate the feasibility of aligning BiT with SimSiam.
1 code implementation • 17 Feb 2021 • Xing Li, Haichun Yang, Jiaxin He, Aadarsh Jha, Agnes B. Fogo, Lee E. Wheless, Shilin Zhao, Yuankai Huo
Reducing outcome variance is an essential task in deep learning based medical image analysis.
no code implementations • 3 Jan 2021 • Quan Liu, Isabella M. Gaeta, Mengyang Zhao, Ruining Deng, Aadarsh Jha, Bryan A. Millis, Anita Mahadevan-Jansen, Matthew J. Tyska, Yuankai Huo
Contribution: The contribution of this paper is three-fold: (1) the proposed method aggregates adversarial simulations and single-stage pixel-embedding based deep learning; (2) the method is assessed with both the cellular (i. e., HeLa cells) and subcellular (i. e., microvilli) objects; and (3) to the best of our knowledge, this is the first study to explore annotation-free instance segmentation and tracking study for microscope videos.
1 code implementation • 2 Nov 2020 • Ruining Deng, Quan Liu, Shunxing Bao, Aadarsh Jha, Catie Chang, Bryan A. Millis, Matthew J. Tyska, Yuankai Huo
Our contribution is three-fold: (1) we approach the weakly supervised segmentation from a novel codebook learning perspective; (2) the CaCL algorithm segments diffuse image patterns rather than focal objects; and (3) the proposed algorithm is implemented in a multi-task framework based on Vector Quantised-Variational AutoEncoder (VQ-VAE) via joint image reconstruction, classification, feature embedding, and segmentation.
no code implementations • 2 Nov 2020 • Quan Liu, Isabella M. Gaeta, Mengyang Zhao, Ruining Deng, Aadarsh Jha, Bryan A. Millis, Anita Mahadevan-Jansen, Matthew J. Tyska, Yuankai Huo
Instance object segmentation and tracking provide comprehensive quantification of objects across microscope videos.
1 code implementation • 28 Jul 2020 • Mengyang Zhao, Aadarsh Jha, Quan Liu, Bryan A. Millis, Anita Mahadevan-Jansen, Le Lu, Bennett A. Landman, Matthew J. Tyskac, Yuankai Huo
With both embedding simulation and empirical validation via the four cohorts from the ISBI cell tracking challenge, the proposed Faster Mean-shift algorithm achieved 7-10 times speedup compared to the state-of-the-art embedding based cell instance segmentation and tracking algorithm.
2 code implementations • 7 Jul 2020 • Aadarsh Jha, Haichun Yang, Ruining Deng, Meghan E. Kapp, Agnes B. Fogo, Yuankai Huo
In this paper, we assess if the end-to-end instance segmentation framework is optimal for high-resolution WSI objects by comparing Mask-RCNN with our proposed detect-then-segment framework.
1 code implementation • 10 Jun 2020 • Ruining Deng, Haichun Yang, Aadarsh Jha, Yuzhe Lu, Peng Chu, Agnes B. Fogo, Yuankai Huo
However, the 3D identification and association of large-scale glomeruli on renal pathology is challenging due to large tissue deformation, missing tissues, and artifacts from WSI.