pwc-archive/papers-with-abstracts huggingface dataset:
Explicit Residual-Based Scalable Image Coding for Humans and Machines
Authors: Yui Tatsumi, Ziyue Zeng, Hiroshi Watanabe
Date: 2025-06-24 00:00:00
Tasks: Image Compression

Scalable image compression is a technique that progressively reconstructs multiple versions of an image for different requirements. In recent years, images have increasingly been consumed not only by humans but also by image recognition models. This shift has drawn growing attention to scalable image compression methods that serve both machine and human vision (ICMH). Many existing models employ neural network-based codecs, known as learned image compression, and have made significant strides in this field by carefully designing the loss functions. In some cases, however, models are overly reliant on their learning capacity, and their architectural design is not sufficiently considered. In this paper, we enhance the coding efficiency and interpretability of ICMH framework by integrating an explicit residual compression mechanism, which is commonly employed in resolution scalable coding methods such as JPEG2000. Specifically, we propose two complementary methods: Feature Residual-based Scalable Coding (FR-ICMH) and Pixel Residual-based Scalable Coding (PR-ICMH). These proposed methods are applicable to various machine vision tasks. Moreover, they provide flexibility to choose between encoder complexity and compression performance, making it adaptable to diverse application requirements. Experimental results demonstrate the effectiveness of our proposed methods, with PR-ICMH achieving up to 29.57% BD-rate savings over the previous work.
Dataset of soil images with corresponding particle size distributions for photogranulometry
Authors: Thomas Plante St-Cyr, François Duhaime, Jean-Sébastien Dubé, Simon Grenier
Date: 2025-06-20 00:00:00

Traditional particle size distribution (PSD) analyses create significant downtime and are expensive in labor and maintenance. These drawbacks could be alleviated using optical grain size analysis integrated into routine geotechnical laboratory workflow. This paper presents a high-resolution dataset of 12,714 images of 321 different soil samples collected in the Montreal, Quebec region, alongside their PSD analysis. It is designed to provide a robust starting point for training convolutional neural networks (CNN) in geotechnical applications. Soil samples were photographed in a standardized top-view position with a resolution of 45 MP and a minimum scale of 39.4 micrometers per pixel, both in their moist and dry states. A custom test bench employing 13x9 inch white aluminum trays, on which the samples are spread in a thin layer, was used. For samples exceeding a size limit, a coning and quartering method was employed for mass reduction.
Convergent and divergent connectivity patterns of the arcuate fasciculus in macaques and humans
Authors: Jiahao Huang, Ruifeng Li, Wenwen Yu, Anan Li, Xiangning Li, Mingchao Yan, Lei Xie, Qingrun Zeng, Xueyan Jia, Shuxin Wang, Ronghui Ju, Feng Chen, Qingming Luo, Hui Gong, Xiaoquan Yang, Yuanjing Feng, Zheng Wang
Date: 2025-06-24 00:00:00
Tasks: Anatomy, Diffusion  MRI

The organization and connectivity of the arcuate fasciculus (AF) in nonhuman primates remain contentious, especially concerning how its anatomy diverges from that of humans. Here, we combined cross-scale single-neuron tracing - using viral-based genetic labeling and fluorescence micro-optical sectioning tomography in macaques (n = 4; age 3 - 11 years) - with whole-brain tractography from 11.7T diffusion MRI. Complemented by spectral embedding analysis of 7.0T MRI in humans, we performed a comparative connectomic analysis of the AF across species. We demonstrate that the macaque AF originates in the temporal-parietal cortex, traverses the auditory cortex and parietal operculum, and projects into prefrontal regions. In contrast, the human AF exhibits greater expansion into the middle temporal gyrus and stronger prefrontal and parietal operculum connectivity - divergences quantified by Kullback-Leibler analysis that likely underpin the evolutionary specialization of human language networks. These interspecies differences - particularly the human AF's broader temporal integration and strengthened frontoparietal linkages - suggest a connectivity-based substrate for the emergence of advanced language processing unique to humans. Furthermore, our findings offer a neuroanatomical framework for understanding AF-related disorders such as aphasia and dyslexia, where aberrant connectivity disrupts language function.
Quantitative Benchmarking of Anomaly Detection Methods in Digital Pathology
Authors: Can Cui, Xindong Zheng, Ruining Deng, Quan Liu, Tianyuan Yao, Keith T Wilson, Lori A Coburn, Bennett A Landman, Haichun Yang, Yaohong Wang, Yuankai Huo
Date: 2025-06-24 00:00:00
Tasks: Anomaly Detection, Artifact Detection, Benchmarking

Anomaly detection has been widely studied in the context of industrial defect inspection, with numerous methods developed to tackle a range of challenges. In digital pathology, anomaly detection holds significant potential for applications such as rare disease identification, artifact detection, and biomarker discovery. However, the unique characteristics of pathology images, such as their large size, multi-scale structures, stain variability, and repetitive patterns, introduce new challenges that current anomaly detection algorithms struggle to address. In this quantitative study, we benchmark over 20 classical and prevalent anomaly detection methods through extensive experiments. We curated five digital pathology datasets, both real and synthetic, to systematically evaluate these approaches. Our experiments investigate the influence of image scale, anomaly pattern types, and training epoch selection strategies on detection performance. The results provide a detailed comparison of each method's strengths and limitations, establishing a comprehensive benchmark to guide future research in anomaly detection for digital pathology images.
Deformable Medical Image Registration with Effective Anatomical Structure Representation and Divide-and-Conquer Network
Authors: Xinke Ma, Yongsheng Pan, Qingjie Zeng, Mengkang Lu, Bolysbek Murat Yerzhanuly, Bazargul Matkerim, Yong Xia
Date: 2025-06-24 00:00:00
Tasks: Deformable Medical Image Registration, Hippocampus, Image Registration, Medical Image Registration

Effective representation of Regions of Interest (ROI) and independent alignment of these ROIs can significantly enhance the performance of deformable medical image registration (DMIR). However, current learning-based DMIR methods have limitations. Unsupervised techniques disregard ROI representation and proceed directly with aligning pairs of images, while weakly-supervised methods heavily depend on label constraints to facilitate registration. To address these issues, we introduce a novel ROI-based registration approach named EASR-DCN. Our method represents medical images through effective ROIs and achieves independent alignment of these ROIs without requiring labels. Specifically, we first used a Gaussian mixture model for intensity analysis to represent images using multiple effective ROIs with distinct intensities. Furthermore, we propose a novel Divide-and-Conquer Network (DCN) to process these ROIs through separate channels to learn feature alignments for each ROI. The resultant correspondences are seamlessly integrated to generate a comprehensive displacement vector field. Extensive experiments were performed on three MRI and one CT datasets to showcase the superior accuracy and deformation reduction efficacy of our EASR-DCN. Compared to VoxelMorph, our EASR-DCN achieved improvements of 10.31\% in the Dice score for brain MRI, 13.01\% for cardiac MRI, and 5.75\% for hippocampus MRI, highlighting its promising potential for clinical applications. The code for this work will be released upon acceptance of the paper.
VHU-Net: Variational Hadamard U-Net for Body MRI Bias Field Correction
Authors: Xin Zhu
Date: 2025-06-23 00:00:00
Tasks: Computational Efficiency, Decoder, Variational Inference

Bias field artifacts in magnetic resonance imaging (MRI) scans introduce spatially smooth intensity inhomogeneities that degrade image quality and hinder downstream analysis. To address this challenge, we propose a novel variational Hadamard U-Net (VHU-Net) for effective body MRI bias field correction. The encoder comprises multiple convolutional Hadamard transform blocks (ConvHTBlocks), each integrating convolutional layers with a Hadamard transform (HT) layer. Specifically, the HT layer performs channel-wise frequency decomposition to isolate low-frequency components, while a subsequent scaling layer and semi-soft thresholding mechanism suppress redundant high-frequency noise. To compensate for the HT layer's inability to model inter-channel dependencies, the decoder incorporates an inverse HT-reconstructed transformer block, enabling global, frequency-aware attention for the recovery of spatially consistent bias fields. The stacked decoder ConvHTBlocks further enhance the capacity to reconstruct the underlying ground-truth bias field. Building on the principles of variational inference, we formulate a new evidence lower bound (ELBO) as the training objective, promoting sparsity in the latent space while ensuring accurate bias field estimation. Comprehensive experiments on abdominal and prostate MRI datasets demonstrate the superiority of VHU-Net over existing state-of-the-art methods in terms of intensity uniformity, signal fidelity, and tissue contrast. Moreover, the corrected images yield substantial downstream improvements in segmentation accuracy. Our framework offers computational efficiency, interpretability, and robust performance across multi-center datasets, making it suitable for clinical deployment.
A Deep Learning Based Method for Fast Registration of Cardiac Magnetic Resonance Images
Authors: Benjamin Graham
Date: 2025-06-23 00:00:00
Tasks: Image Registration, Medical Image Analysis

Image registration is used in many medical image analysis applications, such as tracking the motion of tissue in cardiac images, where cardiac kinematics can be an indicator of tissue health. Registration is a challenging problem for deep learning algorithms because ground truth transformations are not feasible to create, and because there are potentially multiple transformations that can produce images that appear correlated with the goal. Unsupervised methods have been proposed to learn to predict effective transformations, but these methods take significantly longer to predict than established baseline methods. For a deep learning method to see adoption in wider research and clinical settings, it should be designed to run in a reasonable time on common, mid-level hardware. Fast methods have been proposed for the task of image registration but often use patch-based methods which can affect registration accuracy for a highly dynamic organ such as the heart. In this thesis, a fast, volumetric registration model is proposed for the use of quantifying cardiac strain. The proposed Deep Learning Neural Network (DLNN) is designed to utilize an architecture that can compute convolutions incredibly efficiently, allowing the model to achieve registration fidelity similar to other state-of-the-art models while taking a fraction of the time to perform inference. The proposed fast and lightweight registration (FLIR) model is used to predict tissue motion which is then used to quantify the non-uniform strain experienced by the tissue. For acquisitions taken from the same patient at approximately the same time, it would be expected that strain values measured between the acquisitions would have very small differences. Using this metric, strain values computed using the FLIR method are shown to be very consistent.
Staining normalization in histopathology: Method benchmarking using multicenter dataset
Authors: Umair Khan, Jouni Härkönen, Marjukka Friman, Leena Latonen, Teijo Kuopio, Pekka Ruusuvuori
Date: 2025-06-23 00:00:00
Tasks: Benchmarking

Hematoxylin and Eosin (H&E) has been the gold standard in tissue analysis for decades, however, tissue specimens stained in different laboratories vary, often significantly, in appearance. This variation poses a challenge for both pathologists' and AI-based downstream analysis. Minimizing stain variation computationally is an active area of research. To further investigate this problem, we collected a unique multi-center tissue image dataset, wherein tissue samples from colon, kidney, and skin tissue blocks were distributed to 66 different labs for routine H&E staining. To isolate staining variation, other factors affecting the tissue appearance were kept constant. Further, we used this tissue image dataset to compare the performance of eight different stain normalization methods, including four traditional methods, namely, histogram matching, Macenko, Vahadane, and Reinhard normalization, and two deep learning-based methods namely CycleGAN and Pixp2pix, both with two variants each. We used both quantitative and qualitative evaluation to assess the performance of these methods. The dataset's inter-laboratory staining variation could also guide strategies to improve model generalizability through varied training data
Temporal Neural Cellular Automata: Application to modeling of contrast enhancement in breast MRI
Authors: Daniel M. Lang, Richard Osuala, Veronika Spieker, Karim Lekadir, Rickmer Braren, Julia A. Schnabel
Date: 2025-06-23 00:00:00

Synthetic contrast enhancement offers fast image acquisition and eliminates the need for intravenous injection of contrast agent. This is particularly beneficial for breast imaging, where long acquisition times and high cost are significantly limiting the applicability of magnetic resonance imaging (MRI) as a widespread screening modality. Recent studies have demonstrated the feasibility of synthetic contrast generation. However, current state-of-the-art (SOTA) methods lack sufficient measures for consistent temporal evolution. Neural cellular automata (NCA) offer a robust and lightweight architecture to model evolving patterns between neighboring cells or pixels. In this work we introduce TeNCA (Temporal Neural Cellular Automata), which extends and further refines NCAs to effectively model temporally sparse, non-uniformly sampled imaging data. To achieve this, we advance the training strategy by enabling adaptive loss computation and define the iterative nature of the method to resemble a physical progression in time. This conditions the model to learn a physiologically plausible evolution of contrast enhancement. We rigorously train and test TeNCA on a diverse breast MRI dataset and demonstrate its effectiveness, surpassing the performance of existing methods in generation of images that align with ground truth post-contrast sequences.
MedTVT-R1: A Multimodal LLM Empowering Medical Reasoning and Diagnosis
Authors: Yuting Zhang, Kaishen Yuan, Hao Lu, Yutao Yue, Jintai Chen, Kaishun Wu
Date: 2025-06-23 00:00:00
Tasks: Diagnostic, Large Language Model, Multimodal Large Language Model

Accurate and interpretable multi-disease diagnosis remains a critical challenge in medical research, particularly when leveraging heterogeneous multimodal medical data. Current approaches often rely on single-modal data, limiting their ability to comprehensively understand complex diseases. To address this, we propose MedTVT-R1, a novel Multimodal Large Language Model (MLLM) framework designed to integrate clinical multimodal data for reasoning and diagnosing multiple diseases. We construct MedTVT-QA, a curated instruction dataset that provides question-answer pairs for physiological-level interpretations and disease-level diagnoses with a Chain of Evidence approach. MedTVT-R1 incorporates a modality perception layer to capture inter-modal dependencies and adaptively weight modality contributions. Additionally, we employ Group Relative Policy Optimization (GRPO)-based Reinforcement Fine-Tuning with a Jaccard Reward function to enhance diagnostic reasoning. Experimental results demonstrate MedTVT-R1's superiority in multimodal feature utilization and multi-disease diagnosis, offering significant potential for clinical applications such as diagnostic report generation and comorbidity reasoning. The dataset and code are available at https://github.com/keke-nice/MedTVT-R1.
GANs vs. Diffusion Models for virtual staining with the HER2match dataset
Authors: Pascal Klöckner, José Teixeira, Diana Montezuma, Jaime S. Cardoso, Hugo M. Horlings, Sara P. Oliveira
Date: 2025-06-23 00:00:00
Tasks: Virtual Staining

Virtual staining is a promising technique that uses deep generative models to recreate histological stains, providing a faster and more cost-effective alternative to traditional tissue chemical staining. Specifically for H&E-HER2 staining transfer, despite a rising trend in publications, the lack of sufficient public datasets has hindered progress in the topic. Additionally, it is currently unclear which model frameworks perform best for this particular task. In this paper, we introduce the HER2match dataset, the first publicly available dataset with the same breast cancer tissue sections stained with both H&E and HER2. Furthermore, we compare the performance of several Generative Adversarial Networks (GANs) and Diffusion Models (DMs), and implement a novel Brownian Bridge Diffusion Model for H&E-HER2 translation. Our findings indicate that, overall, GANs perform better than DMs, with only the BBDM achieving comparable results. Furthermore, we emphasize the importance of data alignment, as all models trained on HER2match produced vastly improved visuals compared to the widely used consecutive-slide BCI dataset. This research provides a new high-quality dataset ([available upon publication acceptance]), improving both model training and evaluation. In addition, our comparison of frameworks offers valuable guidance for researchers working on the topic.
A Deep Convolutional Neural Network-Based Novel Class Balancing for Imbalance Data Segmentation
Authors: Atifa Kalsoom, M. A. Iftikhar, Amjad Ali, Zubair Shah, Shidin Balakrishnan, Hazrat Ali
Date: 2025-06-23 00:00:00
Tasks: Specificity

Retinal fundus images provide valuable insights into the human eye's interior structure and crucial features, such as blood vessels, optic disk, macula, and fovea. However, accurate segmentation of retinal blood vessels can be challenging due to imbalanced data distribution and varying vessel thickness. In this paper, we propose BLCB-CNN, a novel pipeline based on deep learning and bi-level class balancing scheme to achieve vessel segmentation in retinal fundus images. The BLCB-CNN scheme uses a Convolutional Neural Network (CNN) architecture and an empirical approach to balance the distribution of pixels across vessel and non-vessel classes and within thin and thick vessels. Level-I is used for vessel/non-vessel balancing and Level-II is used for thick/thin vessel balancing. Additionally, pre-processing of the input retinal fundus image is performed by Global Contrast Normalization (GCN), Contrast Limited Adaptive Histogram Equalization (CLAHE), and gamma corrections to increase intensity uniformity as well as to enhance the contrast between vessels and background pixels. The resulting balanced dataset is used for classification-based segmentation of the retinal vascular tree. We evaluate the proposed scheme on standard retinal fundus images and achieve superior performance measures, including an area under the ROC curve of 98.23%, Accuracy of 96.22%, Sensitivity of 81.57%, and Specificity of 97.65%. We also demonstrate the method's efficacy through external cross-validation on STARE images, confirming its generalization ability.
SafeClick: Error-Tolerant Interactive Segmentation of Any Medical Volumes via Hierarchical Expert Consensus
Authors: Yifan Gao, Jiaxi Sheng, Wenbin Wu, Haoyue Li, Yaoxian Dong, Chaoyang Ge, Feng Yuan, Xin Gao
Date: 2025-06-23 00:00:00
Tasks: Image Segmentation, Interactive Segmentation, Medical Image Segmentation, Segmentation, Semantic Segmentation, Volumetric Medical Image Segmentation

Foundation models for volumetric medical image segmentation have emerged as powerful tools in clinical workflows, enabling radiologists to delineate regions of interest through intuitive clicks. While these models demonstrate promising capabilities in segmenting previously unseen anatomical structures, their performance is strongly influenced by prompt quality. In clinical settings, radiologists often provide suboptimal prompts, which affects segmentation reliability and accuracy. To address this limitation, we present SafeClick, an error-tolerant interactive segmentation approach for medical volumes based on hierarchical expert consensus. SafeClick operates as a plug-and-play module compatible with foundation models including SAM 2 and MedSAM 2. The framework consists of two key components: a collaborative expert layer (CEL) that generates diverse feature representations through specialized transformer modules, and a consensus reasoning layer (CRL) that performs cross-referencing and adaptive integration of these features. This architecture transforms the segmentation process from a prompt-dependent operation to a robust framework capable of producing accurate results despite imperfect user inputs. Extensive experiments across 15 public datasets demonstrate that our plug-and-play approach consistently improves the performance of base foundation models, with particularly significant gains when working with imperfect prompts. The source code is available at https://github.com/yifangao112/SafeClick.
Taming Vision-Language Models for Medical Image Analysis: A Comprehensive Review
Authors: Haoneng Lin, Cheng Xu, Jing Qin
Date: 2025-06-23 00:00:00
Tasks: Medical Image Analysis, Prompt Learning

Modern Vision-Language Models (VLMs) exhibit unprecedented capabilities in cross-modal semantic understanding between visual and textual modalities. Given the intrinsic need for multi-modal integration in clinical applications, VLMs have emerged as a promising solution for a wide range of medical image analysis tasks. However, adapting general-purpose VLMs to medical domain poses numerous challenges, such as large domain gaps, complicated pathological variations, and diversity and uniqueness of different tasks. The central purpose of this review is to systematically summarize recent advances in adapting VLMs for medical image analysis, analyzing current challenges, and recommending promising yet urgent directions for further investigations. We begin by introducing core learning strategies for medical VLMs, including pretraining, fine-tuning, and prompt learning. We then categorize five major VLM adaptation strategies for medical image analysis. These strategies are further analyzed across eleven medical imaging tasks to illustrate their current practical implementations. Furthermore, we analyze key challenges that impede the effective adaptation of VLMs to clinical applications and discuss potential directions for future research. We also provide an open-access repository of related literature to facilitate further research, available at https://github.com/haonenglin/Awesome-VLM-for-MIA. It is anticipated that this article can help researchers who are interested in harnessing VLMs in medical image analysis tasks have a better understanding on their capabilities and limitations, as well as current technical barriers, to promote their innovative, robust, and safe application in clinical practice.