arXiv subjects

Shunxing Bao

Publications and source records attributed to Shunxing Bao.

At least 37 records · Page 2Linked to original sources

arXiv2024

HATs: Hierarchical Adaptive Taxonomy Segmentation for Panoramic Pathology Image Analysis

Panoramic image segmentation in computational pathology presents a remarkable challenge due to the morphologically complex and variably scaled anatomy. For instance, the intricate organization in kidney pathology spans multiple layers, from regions like the cortex and medulla to functional units such as glomeruli, tubules, and vessels, down to various cell types. In this paper, we propose a novel Hierarchical Adaptive Taxonomy Segmentation (HATs) method, which is designed to thoroughly segment panoramic views of kidney structures by leveraging detailed anatomical insights. Our approach entails (1) the innovative HATs technique which translates spatial relationships among 15 distinct object classes into a versatile "plug-and-play" loss function that spans across regions, functional units, and cells, (2) the incorporation of anatomical hierarchies and scale considerations into a unified simple matrix representation for all panoramic entities, (3) the adoption of the latest AI foundation model (EfficientSAM) as a feature extraction tool to boost the model's adaptability, yet eliminating the need for manual prompt generation in conventional segment anything model (SAM). Experimental findings demonstrate that the HATs method offers an efficient and effective strategy for integrating clinical insights and imaging precedents into a unified segmentation model across more than 15 categories. The official implementation is publicly available at https://github.com/hrlblab/HATs.

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arXiv2024

Data-driven Nucleus Subclassification on Colon H&E using Style-transferred Digital Pathology

Understanding the way cells communicate, co-locate, and interrelate is essential to furthering our understanding of how the body functions. H&E is widely available, however, cell subtyping often requires expert knowledge and the use of specialized stains. To reduce the annotation burden, AI has been proposed for the classification of cells on H&E. For example, the recent Colon Nucleus Identification and Classification (CoNIC) Challenge focused on labeling 6 cell types on H&E of the colon. However, the CoNIC Challenge was unable to classify epithelial subtypes (progenitor, enteroendocrine, goblet), lymphocyte subtypes (B, helper T, cytotoxic T), and connective subtypes (fibroblasts). We use inter-modality learning to label previously un-labelable cell types on H&E. We take advantage of multiplexed immunofluorescence (MxIF) histology to label 14 cell subclasses. We performed style transfer on the same MxIF tissues to synthesize realistic virtual H&E which we paired with the MxIF-derived cell subclassification labels. We evaluated the efficacy of using a supervised learning scheme where the input was realistic-quality virtual H&E and the labels were MxIF-derived cell subclasses. We assessed our model on private virtual H&E and public real H&E. On virtual H&E, we were able to classify helper T cells and epithelial progenitors with positive predictive values of $0.34 \pm 0.15$ (prevalence $0.03 \pm 0.01$) and $0.47 \pm 0.1$ (prevalence $0.07 \pm 0.02$) respectively, when using ground truth centroid information. On real H&E we could classify helper T cells and epithelial progenitors with upper bound positive predictive values of $0.43 \pm 0.03$ (parent class prevalence 0.21) and $0.94 \pm 0.02$ (parent class prevalence 0.49) when using ground truth centroid information. This is the first work to provide cell type classification for helper T and epithelial progenitor nuclei on H&E.

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arXiv2024

Enhancing Hierarchical Transformers for Whole Brain Segmentation with Intracranial Measurements Integration

Whole brain segmentation with magnetic resonance imaging (MRI) enables the non-invasive measurement of brain regions, including total intracranial volume (TICV) and posterior fossa volume (PFV). Enhancing the existing whole brain segmentation methodology to incorporate intracranial measurements offers a heightened level of comprehensiveness in the analysis of brain structures. Despite its potential, the task of generalizing deep learning techniques for intracranial measurements faces data availability constraints due to limited manually annotated atlases encompassing whole brain and TICV/PFV labels. In this paper, we enhancing the hierarchical transformer UNesT for whole brain segmentation to achieve segmenting whole brain with 133 classes and TICV/PFV simultaneously. To address the problem of data scarcity, the model is first pretrained on 4859 T1-weighted (T1w) 3D volumes sourced from 8 different sites. These volumes are processed through a multi-atlas segmentation pipeline for label generation, while TICV/PFV labels are unavailable. Subsequently, the model is finetuned with 45 T1w 3D volumes from Open Access Series Imaging Studies (OASIS) where both 133 whole brain classes and TICV/PFV labels are available. We evaluate our method with Dice similarity coefficients(DSC). We show that our model is able to conduct precise TICV/PFV estimation while maintaining the 132 brain regions performance at a comparable level. Code and trained model are available at: https://github.com/MASILab/UNesT/tree/main/wholebrainSeg.

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arXiv2024

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. Multi-instance learning (MIL) is a common solution for working with high resolution images by classifying bags of objects (i.e. sets of smaller image patches). However, such processing is typically performed at a single scale (e.g., 20x magnification) of WSIs, disregarding the vital inter-scale information that is key to diagnoses by human pathologists. In this study, we propose a novel cross-scale MIL algorithm to explicitly aggregate inter-scale relationships into a single MIL network for pathological image diagnosis. The contribution of this paper is three-fold: (1) A novel cross-scale MIL (CS-MIL) algorithm that integrates the multi-scale information and the inter-scale relationships is proposed; (2) A toy dataset with scale-specific morphological features is created and released to examine and visualize differential cross-scale attention; (3) Superior performance on both in-house and public datasets is demonstrated by our simple cross-scale MIL strategy. The official implementation is publicly available at https://github.com/hrlblab/CS-MIL.

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arXiv2024

Nucleus subtype classification using inter-modality learning

Understanding the way cells communicate, co-locate, and interrelate is essential to understanding human physiology. Hematoxylin and eosin (H&E) staining is ubiquitously available both for clinical studies and research. The Colon Nucleus Identification and Classification (CoNIC) Challenge has recently innovated on robust artificial intelligence labeling of six cell types on H&E stains of the colon. However, this is a very small fraction of the number of potential cell classification types. Specifically, the CoNIC Challenge is unable to classify epithelial subtypes (progenitor, endocrine, goblet), lymphocyte subtypes (B, helper T, cytotoxic T), or connective subtypes (fibroblasts, stromal). In this paper, we propose to use inter-modality learning to label previously un-labelable cell types on virtual H&E. We leveraged multiplexed immunofluorescence (MxIF) histology imaging to identify 14 subclasses of cell types. We performed style transfer to synthesize virtual H&E from MxIF and transferred the higher density labels from MxIF to these virtual H&E images. We then evaluated the efficacy of learning in this approach. We identified helper T and progenitor nuclei with positive predictive values of $0.34 \pm 0.15$ (prevalence $0.03 \pm 0.01$) and $0.47 \pm 0.1$ (prevalence $0.07 \pm 0.02$) respectively on virtual H&E. This approach represents a promising step towards automating annotation in digital pathology.

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arXiv2024

Inter-vendor harmonization of Computed Tomography (CT) reconstruction kernels using unpaired image translation

The reconstruction kernel in computed tomography (CT) generation determines the texture of the image. Consistency in reconstruction kernels is important as the underlying CT texture can impact measurements during quantitative image analysis. Harmonization (i.e., kernel conversion) minimizes differences in measurements due to inconsistent reconstruction kernels. Existing methods investigate harmonization of CT scans in single or multiple manufacturers. However, these methods require paired scans of hard and soft reconstruction kernels that are spatially and anatomically aligned. Additionally, a large number of models need to be trained across different kernel pairs within manufacturers. In this study, we adopt an unpaired image translation approach to investigate harmonization between and across reconstruction kernels from different manufacturers by constructing a multipath cycle generative adversarial network (GAN). We use hard and soft reconstruction kernels from the Siemens and GE vendors from the National Lung Screening Trial dataset. We use 50 scans from each reconstruction kernel and train a multipath cycle GAN. To evaluate the effect of harmonization on the reconstruction kernels, we harmonize 50 scans each from Siemens hard kernel, GE soft kernel and GE hard kernel to a reference Siemens soft kernel (B30f) and evaluate percent emphysema. We fit a linear model by considering the age, smoking status, sex and vendor and perform an analysis of variance (ANOVA) on the emphysema scores. Our approach minimizes differences in emphysema measurement and highlights the impact of age, sex, smoking status and vendor on emphysema quantification.

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arXiv2023

DeformUX-Net: Exploring a 3D Foundation Backbone for Medical Image Segmentation with Depthwise Deformable Convolution

The application of 3D ViTs to medical image segmentation has seen remarkable strides, somewhat overshadowing the budding advancements in Convolutional Neural Network (CNN)-based models. Large kernel depthwise convolution has emerged as a promising technique, showcasing capabilities akin to hierarchical transformers and facilitating an expansive effective receptive field (ERF) vital for dense predictions. Despite this, existing core operators, ranging from global-local attention to large kernel convolution, exhibit inherent trade-offs and limitations (e.g., global-local range trade-off, aggregating attentional features). We hypothesize that deformable convolution can be an exploratory alternative to combine all advantages from the previous operators, providing long-range dependency, adaptive spatial aggregation and computational efficiency as a foundation backbone. In this work, we introduce 3D DeformUX-Net, a pioneering volumetric CNN model that adeptly navigates the shortcomings traditionally associated with ViTs and large kernel convolution. Specifically, we revisit volumetric deformable convolution in depth-wise setting to adapt long-range dependency with computational efficiency. Inspired by the concepts of structural re-parameterization for convolution kernel weights, we further generate the deformable tri-planar offsets by adapting a parallel branch (starting from $1\times1\times1$ convolution), providing adaptive spatial aggregation across all channels. Our empirical evaluations reveal that the 3D DeformUX-Net consistently outperforms existing state-of-the-art ViTs and large kernel convolution models across four challenging public datasets, spanning various scales from organs (KiTS: 0.680 to 0.720, MSD Pancreas: 0.676 to 0.717, AMOS: 0.871 to 0.902) to vessels (e.g., MSD hepatic vessels: 0.635 to 0.671) in mean Dice.

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arXiv2023

Deep conditional generative models for longitudinal single-slice abdominal computed tomography harmonization

Two-dimensional single-slice abdominal computed tomography (CT) provides a detailed tissue map with high resolution allowing quantitative characterization of relationships between health conditions and aging. However, longitudinal analysis of body composition changes using these scans is difficult due to positional variation between slices acquired in different years, which leading to different organs/tissues captured. To address this issue, we propose C-SliceGen, which takes an arbitrary axial slice in the abdominal region as a condition and generates a pre-defined vertebral level slice by estimating structural changes in the latent space. Our experiments on 2608 volumetric CT data from two in-house datasets and 50 subjects from the 2015 Multi-Atlas Abdomen Labeling Challenge dataset (BTCV) Challenge demonstrate that our model can generate high-quality images that are realistic and similar. We further evaluate our method's capability to harmonize longitudinal positional variation on 1033 subjects from the Baltimore Longitudinal Study of Aging (BLSA) dataset, which contains longitudinal single abdominal slices, and confirmed that our method can harmonize the slice positional variance in terms of visceral fat area. This approach provides a promising direction for mapping slices from different vertebral levels to a target slice and reducing positional variance for single-slice longitudinal analysis. The source code is available at: https://github.com/MASILab/C-SliceGen.

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arXiv2023

UNesT: Local Spatial Representation Learning with Hierarchical Transformer for Efficient Medical Segmentation

Transformer-based models, capable of learning better global dependencies, have recently demonstrated exceptional representation learning capabilities in computer vision and medical image analysis. Transformer reformats the image into separate patches and realizes global communication via the self-attention mechanism. However, positional information between patches is hard to preserve in such 1D sequences, and loss of it can lead to sub-optimal performance when dealing with large amounts of heterogeneous tissues of various sizes in 3D medical image segmentation. Additionally, current methods are not robust and efficient for heavy-duty medical segmentation tasks such as predicting a large number of tissue classes or modeling globally inter-connected tissue structures. To address such challenges and inspired by the nested hierarchical structures in vision transformer, we proposed a novel 3D medical image segmentation method (UNesT), employing a simplified and faster-converging transformer encoder design that achieves local communication among spatially adjacent patch sequences by aggregating them hierarchically. We extensively validate our method on multiple challenging datasets, consisting of multiple modalities, anatomies, and a wide range of tissue classes, including 133 structures in the brain, 14 organs in the abdomen, 4 hierarchical components in the kidneys, inter-connected kidney tumors and brain tumors. We show that UNesT consistently achieves state-of-the-art performance and evaluate its generalizability and data efficiency. Particularly, the model achieves whole brain segmentation task complete ROI with 133 tissue classes in a single network, outperforming prior state-of-the-art method SLANT27 ensembled with 27 networks.

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arXiv2023

Evaluation Kidney Layer Segmentation on Whole Slide Imaging using Convolutional Neural Networks and Transformers

The segmentation of kidney layer structures, including cortex, outer stripe, inner stripe, and inner medulla within human kidney whole slide images (WSI) plays an essential role in automated image analysis in renal pathology. However, the current manual segmentation process proves labor-intensive and infeasible for handling the extensive digital pathology images encountered at a large scale. In response, the realm of digital renal pathology has seen the emergence of deep learning-based methodologies. However, very few, if any, deep learning based approaches have been applied to kidney layer structure segmentation. Addressing this gap, this paper assesses the feasibility of performing deep learning based approaches on kidney layer structure segmetnation. This study employs the representative convolutional neural network (CNN) and Transformer segmentation approaches, including Swin-Unet, Medical-Transformer, TransUNet, U-Net, PSPNet, and DeepLabv3+. We quantitatively evaluated six prevalent deep learning models on renal cortex layer segmentation using mice kidney WSIs. The empirical results stemming from our approach exhibit compelling advancements, as evidenced by a decent Mean Intersection over Union (mIoU) index. The results demonstrate that Transformer models generally outperform CNN-based models. By enabling a quantitative evaluation of renal cortical structures, deep learning approaches are promising to empower these medical professionals to make more informed kidney layer segmentation.

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arXiv2023

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. With the zero-shot segmentation capacity, SAM achieved impressive flexibility and precision on various segmentation tasks. However, the current pipeline requires manual prompts during the inference stage, which is still resource intensive for biomedical image segmentation. In this paper, instead of using prompts during the inference stage, we introduce a pipeline that utilizes the SAM, called all-in-SAM, through the entire AI development workflow (from annotation generation to model finetuning) without requiring manual prompts during the inference stage. Specifically, SAM is first employed to generate pixel-level annotations from weak prompts (e.g., points, bounding box). Then, the pixel-level annotations are used to finetune the SAM segmentation model rather than training from scratch. Our experimental results reveal two key findings: 1) the proposed pipeline surpasses the state-of-the-art (SOTA) methods in a nuclei segmentation task on the public Monuseg dataset, and 2) the utilization of weak and few annotations for SAM finetuning achieves competitive performance compared to using strong pixel-wise annotated data.

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arXiv2023

High-performance Data Management for Whole Slide Image Analysis in Digital Pathology

When dealing with giga-pixel digital pathology in whole-slide imaging, a notable proportion of data records holds relevance during each analysis operation. For instance, when deploying an image analysis algorithm on whole-slide images (WSI), the computational bottleneck often lies in the input-output (I/O) system. This is particularly notable as patch-level processing introduces a considerable I/O load onto the computer system. However, this data management process could be further paralleled, given the typical independence of patch-level image processes across different patches. This paper details our endeavors in tackling this data access challenge by implementing the Adaptable IO System version 2 (ADIOS2). Our focus has been constructing and releasing a digital pathology-centric pipeline using ADIOS2, which facilitates streamlined data management across WSIs. Additionally, we've developed strategies aimed at curtailing data retrieval times. 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"). Our findings reveal noteworthy outcomes. Under the CPU scenario, ADIOS2 showcases an impressive two-fold speed-up compared to the brute-force approach. In the GPU scenario, its performance stands on par with the cutting-edge GPU I/O acceleration framework, NVIDIA Magnum IO GPU Direct Storage (GDS). From what we know, this appears to be among the initial instances, if any, of utilizing ADIOS2 within the field of digital pathology. The source code has been made publicly available at https://github.com/hrlblab/adios.

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arXiv2023

Cell Spatial Analysis in Crohn's Disease: Unveiling Local Cell Arrangement Pattern with Graph-based Signatures

Crohn's disease (CD) is a chronic and relapsing inflammatory condition that affects segments of the gastrointestinal tract. CD activity is determined by histological findings, particularly the density of neutrophils observed on Hematoxylin and Eosin stains (H&E) imaging. However, understanding the broader morphometry and local cell arrangement beyond cell counting and tissue morphology remains challenging. To address this, we characterize six distinct cell types from H&E images and develop a novel approach for the local spatial signature of each cell. Specifically, we create a 10-cell neighborhood matrix, representing neighboring cell arrangements for each individual cell. Utilizing t-SNE for non-linear spatial projection in scatter-plot and Kernel Density Estimation contour-plot formats, our study examines patterns of differences in the cellular environment associated with the odds ratio of spatial patterns between active CD and control groups. This analysis is based on data collected at the two research institutes. The findings reveal heterogeneous nearest-neighbor patterns, signifying distinct tendencies of cell clustering, with a particular focus on the rectum region. These variations underscore the impact of data heterogeneity on cell spatial arrangements in CD patients. Moreover, the spatial distribution disparities between the two research sites highlight the significance of collaborative efforts among healthcare organizations. All research analysis pipeline tools are available at https://github.com/MASILab/cellNN.

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arXiv2023

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. Unfortunately, many prior anomaly detection methods were optimized for a specific "known" abnormality (e.g., brain tumor, bone fraction, cell types). Moreover, even though only the normal images were used in the training process, the abnormal images were often employed during the validation process (e.g., epoch selection, hyper-parameter tuning), which might leak the supposed ``unknown" abnormality unintentionally. In this study, we investigated these two essential aspects regarding universal anomaly detection in medical images by (1) comparing various anomaly detection methods across four medical datasets, (2) investigating the inevitable but often neglected issues on how to unbiasedly select the optimal anomaly detection model during the validation phase using only normal images, and (3) proposing a simple decision-level ensemble method to leverage the advantage of different kinds of anomaly detection without knowing the abnormality. The results of our experiments indicate that none of the evaluated methods consistently achieved the best performance across all datasets. Our proposed method enhanced the robustness of performance in general (average AUC 0.956).

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arXiv2023

Multi-scale Multi-site Renal Microvascular Structures Segmentation for Whole Slide Imaging in Renal Pathology

Segmentation of microvascular structures, such as arterioles, venules, and capillaries, from human kidney whole slide images (WSI) has become a focal point in renal pathology. Current manual segmentation techniques are time-consuming and not feasible for large-scale digital pathology images. 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. In this paper, we present Omni-Seg, a novel single dynamic network method that capitalizes on multi-site, multi-scale training data. Unique to our approach, we utilize partially labeled images, where only one tissue type is labeled per training image, to segment microvascular structures. We train a singular deep network using images from two datasets, HuBMAP and NEPTUNE, across different magnifications (40x, 20x, 10x, and 5x). Experimental results indicate that Omni-Seg outperforms in terms of both the Dice Similarity Coefficient (DSC) and Intersection over Union (IoU). Our proposed method provides renal pathologists with a powerful computational tool for the quantitative analysis of renal microvascular structures.

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arXiv2023

Leverage Weakly Annotation to Pixel-wise Annotation via Zero-shot Segment Anything Model for Molecular-empowered Learning

Precise identification of multiple cell classes in high-resolution Giga-pixel whole slide imaging (WSI) is critical for various clinical scenarios. Building an AI model for this purpose typically requires pixel-level annotations, which are often unscalable and must be done by skilled domain experts (e.g., pathologists). However, these annotations can be prone to errors, especially when distinguishing between intricate cell types (e.g., podocytes and mesangial cells) using only visual inspection. Interestingly, a recent study showed that lay annotators, when using extra immunofluorescence (IF) images for reference (referred to as molecular-empowered learning), can sometimes outperform domain experts in labeling. Despite this, the resource-intensive task of manual delineation remains a necessity during the annotation process. 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. Specifically, we harness SAM's ability to produce pixel-level annotations from box annotations and utilize these SAM-generated labels to train a segmentation model. Our findings show that the proposed SAM-assisted molecular-empowered learning (SAM-L) can diminish the labeling efforts for lay annotators by only requiring weak box annotations. This is achieved without compromising annotation accuracy or the performance of the deep learning-based segmentation. This research represents a significant advancement in democratizing the annotation process for training pathological image segmentation, relying solely on non-expert annotators.

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arXiv2023

Scaling Up 3D Kernels with Bayesian Frequency Re-parameterization for Medical Image Segmentation

With the inspiration of vision transformers, the concept of depth-wise convolution revisits to provide a large Effective Receptive Field (ERF) using Large Kernel (LK) sizes for medical image segmentation. However, the segmentation performance might be saturated and even degraded as the kernel sizes scaled up (e.g., $21\times 21\times 21$) in a Convolutional Neural Network (CNN). We hypothesize that convolution with LK sizes is limited to maintain an optimal convergence for locality learning. While Structural Re-parameterization (SR) enhances the local convergence with small kernels in parallel, optimal small kernel branches may hinder the computational efficiency for training. In this work, we propose RepUX-Net, a pure CNN architecture with a simple large kernel block design, which competes favorably with current network state-of-the-art (SOTA) (e.g., 3D UX-Net, SwinUNETR) using 6 challenging public datasets. We derive an equivalency between kernel re-parameterization and the branch-wise variation in kernel convergence. Inspired by the spatial frequency in the human visual system, we extend to vary the kernel convergence into element-wise setting and model the spatial frequency as a Bayesian prior to re-parameterize convolutional weights during training. Specifically, a reciprocal function is leveraged to estimate a frequency-weighted value, which rescales the corresponding kernel element for stochastic gradient descent. From the experimental results, RepUX-Net consistently outperforms 3D SOTA benchmarks with internal validation (FLARE: 0.929 to 0.944), external validation (MSD: 0.901 to 0.932, KiTS: 0.815 to 0.847, LiTS: 0.933 to 0.949, TCIA: 0.736 to 0.779) and transfer learning (AMOS: 0.880 to 0.911) scenarios in Dice Score.

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arXiv2023

Multi-Contrast Computed Tomography Atlas of Healthy Pancreas

With the substantial diversity in population demographics, such as differences in age and body composition, the volumetric morphology of pancreas varies greatly, resulting in distinctive variations in shape and appearance. Such variations increase the difficulty at generalizing population-wide pancreas features. A volumetric spatial reference is needed to adapt the morphological variability for organ-specific analysis. Here, we proposed a high-resolution computed tomography (CT) atlas framework specifically optimized for the pancreas organ across multi-contrast CT. We introduce a deep learning-based pre-processing technique to extract the abdominal region of interests (ROIs) and leverage a hierarchical registration pipeline to align the pancreas anatomy across populations. Briefly, DEEDs affine and non-rigid registration are performed to transfer patient abdominal volumes to a fixed high-resolution atlas template. To generate and evaluate the pancreas atlas template, multi-contrast modality CT scans of 443 subjects (without reported history of pancreatic disease, age: 15-50 years old) are processed. Comparing with different registration state-of-the-art tools, the combination of DEEDs affine and non-rigid registration achieves the best performance for the pancreas label transfer across all contrast phases. We further perform external evaluation with another research cohort of 100 de-identified portal venous scans with 13 organs labeled, having the best label transfer performance of 0.504 Dice score in unsupervised setting. The qualitative representation (e.g., average mapping) of each phase creates a clear boundary of pancreas and its distinctive contrast appearance. The deformation surface renderings across scales (e.g., small to large volume) further illustrate the generalizability of the proposed atlas template.

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