Search Results for author:
Found 40 papers, 25 papers with code
Circle Representation for Medical Instance Object Segmentation
Recently, circle representation has been introduced for medical imaging, designed specifically to enhance the detection of instance objects that are spherically shaped (e. g., cells, glomeruli, and nuclei).
PrPSeg: Universal Proposition Learning for Panoramic Renal Pathology Segmentation
Understanding the anatomy of renal pathology is crucial for advancing disease diagnostics, treatment evaluation, and clinical research.
Nucleus subtype classification using inter-modality learning
In this paper, we propose to use inter-modality learning to label previously un-labelable cell types on virtual H&E.
Evaluation Kidney Layer Segmentation on Whole Slide Imaging using Convolutional Neural Networks and Transformers
However, very few, if any, deep learning based approaches have been applied to kidney layer structure segmentation.
False Negative/Positive Control for SAM on Noisy Medical Images
The method couples multi-box prompt augmentation and an aleatoric uncertainty-based false-negative (FN) and false-positive (FP) correction (FNPC) strategy.
Cell Spatial Analysis in Crohn's Disease: Unveiling Local Cell Arrangement Pattern with Graph-based Signatures
This analysis is based on data collected at the two research institutes.
Cross-modality Attention-based Multimodal Fusion for Non-small Cell Lung Cancer (NSCLC) Patient Survival Prediction
Compared with single modality, which achieved c-index of 0. 5772 and 0. 5885 using solely tissue image data or RNA-seq data, respectively, the proposed fusion approach achieved c-index 0. 6587 in our experiment, showcasing the capability of assimilating modality-specific knowledge from varied modalities.
Eosinophils Instance Object Segmentation on Whole Slide Imaging Using Multi-label Circle Representation
In this paper, we propose the multi-label CircleSnake model for instance segmentation on Eos.
Deep Learning-Based Open Source Toolkit for Eosinophil Detection in Pediatric Eosinophilic Esophagitis
Eosinophilic Esophagitis (EoE) is a chronic, immune/antigen-mediated esophageal disease, characterized by symptoms related to esophageal dysfunction and histological evidence of eosinophil-dominant inflammation.
Spatial Pathomics Toolkit for Quantitative Analysis of Podocyte Nuclei with Histology and Spatial Transcriptomics Data in Renal Pathology
Podocytes, specialized epithelial cells that envelop the glomerular capillaries, play a pivotal role in maintaining renal health.
Multi-scale Multi-site Renal Microvascular Structures Segmentation for Whole Slide Imaging in Renal Pathology
While deep learning-based methods offer a solution for automatic segmentation, most suffer from a limitation: they are designed for and restricted to training on single-site, single-scale data.
High-performance Data Management for Whole Slide Image Analysis in Digital Pathology
The performance evaluation encompasses two key scenarios: (1) a pure CPU-based image analysis scenario ("CPU scenario"), and (2) a GPU-based deep learning framework scenario ("GPU scenario").
Leverage Weakly Annotation to Pixel-wise Annotation via Zero-shot Segment Anything Model for Molecular-empowered Learning
In this paper, we explore the potential of bypassing pixel-level delineation by employing the recent segment anything model (SAM) on weak box annotation in a zero-shot learning approach.
Feasibility of Universal Anomaly Detection without Knowing the Abnormality in Medical Images
Many anomaly detection approaches, especially deep learning methods, have been recently developed to identify abnormal image morphology by only employing normal images during training.
All-in-SAM: from Weak Annotation to Pixel-wise Nuclei Segmentation with Prompt-based Finetuning
The Segment Anything Model (SAM) is a recently proposed prompt-based segmentation model in a generic zero-shot segmentation approach.
Robust Fiber ODF Estimation Using Deep Constrained Spherical Deconvolution for Diffusion MRI
From the experimental results, the proposed data-driven framework outperforms the existing benchmarks in repeated fODF estimation.
Democratizing Pathological Image Segmentation with Lay Annotators via Molecular-empowered Learning
The contribution of this paper is threefold: (1) We proposed a molecular-empowered learning scheme for multi-class cell segmentation using partial labels from lay annotators; (2) The proposed method integrated Giga-pixel level molecular-morphology cross-modality registration, molecular-informed annotation, and molecular-oriented segmentation model, so as to achieve significantly superior performance via 3 lay annotators as compared with 2 experienced pathologists; (3) A deep corrective learning (learning with imperfect label) method is proposed to further improve the segmentation performance using partially annotated noisy data.
An Accelerated Pipeline for Multi-label Renal Pathology Image Segmentation at the Whole Slide Image Level
Our proposed method's innovative contribution is two-fold: (1) a Docker is released for an end-to-end slide-wise multi-tissue segmentation for WSIs; and (2) the pipeline is deployed on a GPU to accelerate the prediction, achieving better segmentation quality in less time.
An End-to-end Pipeline for 3D Slide-wise Multi-stain Renal Pathology Registration
In this paper, we provide a Docker for an end-to-end 3D slide-wise registration pipeline on needle biopsy serial sections in a multi-stain paradigm.
Exploring shared memory architectures for end-to-end gigapixel deep learning
The M1 Ultra SoC was able to train the model directly on gigapixel images (16000$\times$64000 pixels, 1. 024 billion pixels) with a batch size of 1 using over 100 GB of unified memory for the process at an average speed of 1 minute and 21 seconds per batch with Tensorflow 2/Keras.
Segment Anything Model (SAM) for Digital Pathology: Assess Zero-shot Segmentation on Whole Slide Imaging
However, it does not consistently achieve satisfying performance for dense instance object segmentation, even with 20 prompts (clicks/boxes) on each image.
Cross-scale Multi-instance Learning for Pathological Image Diagnosis
Analyzing high resolution whole slide images (WSIs) with regard to information across multiple scales poses a significant challenge in digital pathology.
CircleSnake: Instance Segmentation with Circle Representation
Circle representation has recently been introduced as a medical imaging optimized representation for more effective instance object detection on ball-shaped medical objects.
Compound Figure Separation of Biomedical Images: Mining Large Datasets for Self-supervised Learning
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.
Cross-scale Attention Guided Multi-instance Learning for Crohn's Disease Diagnosis with Pathological Images
Multi-instance learning (MIL) is widely used in the computer-aided interpretation of pathological Whole Slide Images (WSIs) to solve the lack of pixel-wise or patch-wise annotations.
Omni-Seg: A Scale-aware Dynamic Network for Renal Pathological Image Segmentation
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.
Survival Prediction of Brain Cancer with Incomplete Radiology, Pathology, Genomics, and Demographic Data
Thus, there are still open questions on how to effectively predict brain cancer survival from the incomplete radiological, pathological, genomic, and demographic data (e. g., one or more modalities might not be collected for a patient).
Omni-Seg: A Single Dynamic Network for Multi-label Renal Pathology Image Segmentation using Partially Labeled Data
Computer-assisted quantitative analysis on Giga-pixel pathology images has provided a new avenue in histology examination.
Circle Representation for Medical Object Detection
Compared with the conventional bounding box representation, the proposed bounding circle representation innovates in three-fold: (1) it is optimized for ball-shaped biomedical objects; (2) The circle representation reduced the degree of freedom compared with box representation; (3) It is naturally more rotation invariant.
Ranked #1 on
Medical Object Detection
on MoNuSeg 2018
Compound Figure Separation of Biomedical Images with Side Loss
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.
VoxelEmbed: 3D Instance Segmentation and Tracking with Voxel Embedding based Deep Learning
Recently, pixel embedding-based cell instance segmentation and tracking provided a neat and generalizable computing paradigm for understanding cellular dynamics.
SimTriplet: Simple Triplet Representation Learning with a Single GPU
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.
Improve Global Glomerulosclerosis Classification with Imbalanced Data using CircleMix Augmentation
Different from the recently proposed CutMix method, the CircleMix augmentation is optimized for the ball-shaped biomedical objects, such as glomeruli.
ASIST: Annotation-free Synthetic Instance Segmentation and Tracking by Adversarial Simulations
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.
CaCL: Class-aware Codebook Learning for Weakly Supervised Segmentation on Diffuse Image Patterns
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.
ASIST: Annotation-free synthetic instance segmentation and tracking for microscope video analysis
Instance object segmentation and tracking provide comprehensive quantification of objects across microscope videos.
EasierPath: An Open-source Tool for Human-in-the-loop Deep Learning of Renal Pathology
Inspired by the recent "human-in-the-loop" strategy, we developed EasierPath, an open-source tool to integrate human physicians and deep learning algorithms for efficient large-scale pathological image quantification as a loop.
Instance Segmentation for Whole Slide Imaging: End-to-End or Detect-Then-Segment
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.
Map3D: Registration Based Multi-Object Tracking on 3D Serial Whole Slide Images
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.
CircleNet: Anchor-free Detection with Circle Representation
In this work, we propose CircleNet, a simple anchor-free detection method with circle representation for detection of the ball-shaped glomerulus.
