Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention最新文献

{"title":"Gradient Guided Co-Retention Feature Pyramid Network for LDCT Image Denoising.","authors":"Li Zhou, Dayang Wang, Yongshun Xu, Shuo Han, Bahareh Morovati, Shuyi Fan, Hengyong Yu","doi":"10.1007/978-3-031-72390-2_15","DOIUrl":"10.1007/978-3-031-72390-2_15","url":null,"abstract":"<p><p>Low-dose computed tomography (LDCT) reduces the risks of radiation exposure but introduces noise and artifacts into CT images. The Feature Pyramid Network (FPN) is a conventional method for extracting multi-scale feature maps from input images. While upper layers in FPN enhance semantic value, details become generalized with reduced spatial resolution at each layer. In this work, we propose a Gradient Guided Co-Retention Feature Pyramid Network (G2CR-FPN) to address the connection between spatial resolution and semantic value beyond feature maps extracted from LDCT images. The network is structured with three essential paths: the bottom-up path utilizes the FPN structure to generate the hierarchical feature maps, representing multi-scale spatial resolutions and semantic values. Meanwhile, the lateral path serves as a skip connection between feature maps with the same spatial resolution, while also functioning feature maps as directional gradients. This path incorporates a gradient approximation, deriving edge-like enhanced feature maps in horizontal and vertical directions. The top-down path incorporates a proposed co-retention block that learns the high-level semantic value embedded in the preceding map of the path. This learning process is guided by the directional gradient approximation of the high-resolution feature map from the bottom-up path. Experimental results on the clinical CT images demonstrated the promising performance of the model. Our code is available at: https://github.com/liz109/G2CR-FPN.</p>","PeriodicalId":94280,"journal":{"name":"Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention","volume":"15012 ","pages":"153-163"},"PeriodicalIF":0.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12443485/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145088647","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rethinking Histology Slide Digitization Workflows for Low-Resource Settings.","authors":"Talat Zehra, Joseph Marino, Wendy Wang, Grigoriy Frantsuzov, Saad Nadeem","doi":"10.1007/978-3-031-72083-3_40","DOIUrl":"10.1007/978-3-031-72083-3_40","url":null,"abstract":"<p><p>Histology slide digitization is becoming essential for telepathology (remote consultation), knowledge sharing (education), and using the state-of-the-art artificial intelligence algorithms (augmented/automated end-to-end clinical workflows). However, the cumulative costs of digital multi-slide high-speed brightfield scanners, cloud/on-premises storage, and personnel (IT and technicians) make the current slide digitization workflows out-of-reach for limited-resource settings, further widening the health equity gap; even single-slide manual scanning commercial solutions are costly due to hardware requirements (high-resolution cameras, high-spec PC/workstation, and support for only high-end microscopes). In this work, we present a new cloud slide digitization workflow for creating scanner-quality whole-slide images (WSIs) from uploaded low-quality videos, acquired from cheap and inexpensive microscopes with built-in cameras. Specifically, we present a pipeline to create stitched WSIs while automatically deblurring out-of-focus regions, upsampling input 10X images to 40X resolution, and reducing brightness/contrast and light-source illumination variations. We demonstrate the WSI creation efficacy from our workflow on World Health Organization-declared neglected tropical disease, Cutaneous Leishmaniasis (prevalent only in the poorest regions of the world and only diagnosed by sub-specialist dermatopathologists, rare in poor countries), as well as other common pathologies on core biopsies of breast, liver, duodenum, stomach and lymph node. The code and pretrained models will be accessible via our GitHub (https://github.com/nadeemlab/DeepLIIF), and the cloud platform will be available at https://deepliif.org for uploading microscope videos and downloading/viewing WSIs with shareable links (no sign-in required) for telepathology and knowledge sharing.</p>","PeriodicalId":94280,"journal":{"name":"Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention","volume":"15004 ","pages":"427-436"},"PeriodicalIF":0.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11786607/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143082977","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Feature Extraction for Generative Medical Imaging Evaluation: New Evidence Against an Evolving Trend.","authors":"McKell Woodland, Austin Castelo, Mais Al Taie, Jessica Albuquerque Marques Silva, Mohamed Eltaher, Frank Mohn, Alexander Shieh, Suprateek Kundu, Joshua P Yung, Ankit B Patel, Kristy K Brock","doi":"10.1007/978-3-031-72390-2_9","DOIUrl":"10.1007/978-3-031-72390-2_9","url":null,"abstract":"<p><p>Fréchet Inception Distance (FID) is a widely used metric for assessing synthetic image quality. It relies on an ImageNet-based feature extractor, making its applicability to medical imaging unclear. A recent trend is to adapt FID to medical imaging through feature extractors trained on medical images. Our study challenges this practice by demonstrating that ImageNet-based extractors are more consistent and aligned with human judgment than their RadImageNet counterparts. We evaluated sixteen StyleGAN2 networks across four medical imaging modalities and four data augmentation techniques with Fréchet distances (FDs) computed using eleven ImageNet or RadImageNet-trained feature extractors. Comparison with human judgment via visual Turing tests revealed that ImageNet-based extractors produced rankings consistent with human judgment, with the FD derived from the ImageNet-trained SwAV extractor significantly correlating with expert evaluations. In contrast, RadImageNet-based rankings were volatile and inconsistent with human judgment. Our findings challenge prevailing assumptions, providing novel evidence that medical image-trained feature extractors do not inherently improve FDs and can even compromise their reliability. Our code is available at https://github.com/mckellwoodland/fid-med-eval.</p>","PeriodicalId":94280,"journal":{"name":"Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention","volume":"15012 ","pages":"87-97"},"PeriodicalIF":0.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12117514/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144183435","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of Effective Connectome from Infancy to Adolescence.","authors":"Guoshi Li, Kim-Han Thung, Hoyt Taylor, Zhengwang Wu, Gang Li, Li Wang, Weili Lin, Sahar Ahmad, Pew-Thian Yap","doi":"10.1007/978-3-031-72384-1_13","DOIUrl":"10.1007/978-3-031-72384-1_13","url":null,"abstract":"<p><p>Delineating the normative developmental profile of functional connectome is important for both standardized assessment of individual growth and early detection of diseases. However, functional connectome has been mostly studied using functional connectivity (FC), where undirected connectivity strengths are estimated from statistical correlation of resting-state functional MRI (rs-fMRI) signals. To address this limitation, we applied regression dynamic causal modeling (rDCM) to delineate the developmental trajectories of effective connectivity (EC), the directed causal influence among neuronal populations, in whole-brain networks from infancy to adolescence (0-22 years old) based on high-quality rs-fMRI data from Baby Connectome Project (BCP) and Human Connectome Project Development (HCP-D). Analysis with linear mixed model demonstrates significant age effect on the mean nodal EC which is best fit by a \"U\" shaped quadratic curve with minimal EC at around 2 years old. Further analysis indicates that five brain regions including the left and right cuneus, left precuneus, left supramarginal gyrus and right inferior temporal gyrus have the most significant age effect on nodal EC (<i>p</i> < 0.05, FDR corrected). Moreover, the frontoparietal control (FPC) network shows the fastest increase from early childhood to adolescence followed by the visual and salience networks. Our findings suggest complex nonlinear developmental profile of EC from infancy to adolescence, which may reflect dynamic structural and functional maturation during this critical growth period.</p>","PeriodicalId":94280,"journal":{"name":"Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention","volume":"15003 ","pages":"131-140"},"PeriodicalIF":0.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11758277/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143049390","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hallucination Index: An Image Quality Metric for Generative Reconstruction Models.","authors":"Matthew Tivnan, Siyeop Yoon, Zhennong Chen, Xiang Li, Dufan Wu, Quanzheng Li","doi":"10.1007/978-3-031-72117-5_42","DOIUrl":"10.1007/978-3-031-72117-5_42","url":null,"abstract":"<p><p>Generative image reconstruction algorithms such as measurement conditioned diffusion models are increasingly popular in the field of medical imaging. These powerful models can transform low signal-to-noise ratio (SNR) inputs into outputs with the appearance of high SNR. However, the outputs can have a new type of error called hallucinations. In medical imaging, these hallucinations may not be obvious to a Radiologist but could cause diagnostic errors. Generally, hallucination refers to error in estimation of object structure caused by a machine learning model, but there is no widely accepted method to evaluate hallucination magnitude. In this work, we propose a new image quality metric called the hallucination index. Our approach is to compute the Hellinger distance from the distribution of reconstructed images to a zero hallucination reference distribution. To evaluate our approach, we conducted a numerical experiment with electron microscopy images, simulated noisy measurements, and applied diffusion based reconstructions. We sampled the measurements and the generative reconstructions repeatedly to compute the sample mean and covariance. For the zero hallucination reference, we used the forward diffusion process applied to ground truth. Our results show that higher measurement SNR leads to lower hallucination index for the same apparent image quality. We also evaluated the impact of early stopping in the reverse diffusion process and found that more modest denoising strengths can reduce hallucination. We believe this metric could be useful for evaluation of generative image reconstructions or as a warning label to inform radiologists about the degree of hallucinations in medical images.</p>","PeriodicalId":94280,"journal":{"name":"Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention","volume":"15010 ","pages":"449-458"},"PeriodicalIF":0.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956116/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143757111","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Spatial Diffusion for Cell Layout Generation.","authors":"Chen Li, Xiaoling Hu, Shahira Abousamra, Meilong Xu, Chao Chen","doi":"10.1007/978-3-031-72083-3_45","DOIUrl":"10.1007/978-3-031-72083-3_45","url":null,"abstract":"<p><p>Generative models, such as GANs and diffusion models, have been used to augment training sets and boost performances in different tasks. We focus on generative models for cell detection instead, i.e., locating and classifying cells in given pathology images. One important information that has been largely overlooked is the spatial patterns of the cells. In this paper, we propose a spatial-pattern-guided generative model for cell layout generation. Specifically, a novel diffusion model guided by spatial features and generates realistic cell layouts has been proposed. We explore different density models as spatial features for the diffusion model. In downstream tasks, we show that the generated cell layouts can be used to guide the generation of high-quality pathology images. Augmenting with these images can significantly boost the performance of SOTA cell detection methods. The code is available at https://github.com/superlc1995/Diffusion-cell.</p>","PeriodicalId":94280,"journal":{"name":"Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention","volume":"15004 ","pages":"481-491"},"PeriodicalIF":0.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12206494/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144532224","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Interpretable Spatio-Temporal Embedding for Brain Structural-Effective Network with Ordinary Differential Equation.","authors":"Haoteng Tang, Guodong Liu, Siyuan Dai, Kai Ye, Kun Zhao, Wenlu Wang, Carl Yang, Lifang He, Alex Leow, Paul Thompson, Heng Huang, Liang Zhan","doi":"10.1007/978-3-031-72069-7_22","DOIUrl":"10.1007/978-3-031-72069-7_22","url":null,"abstract":"<p><p>The MRI-derived brain network serves as a pivotal instrument in elucidating both the structural and functional aspects of the brain, encompassing the ramifications of diseases and developmental processes. However, prevailing methodologies, often focusing on synchronous BOLD signals from functional MRI (fMRI), may not capture directional influences among brain regions and rarely tackle temporal functional dynamics. In this study, we first construct the brain-effective network via the dynamic causal model. Subsequently, we introduce an interpretable graph learning framework termed Spatio-Temporal Embedding ODE (STE-ODE). This framework incorporates specifically designed directed node embedding layers, aiming at capturing the dynamic inter-play between structural and effective networks via an ordinary differential equation (ODE) model, which characterizes spatial-temporal brain dynamics. Our framework is validated on several clinical phenotype prediction tasks using two independent publicly available datasets (HCP and OASIS). The experimental results clearly demonstrate the advantages of our model compared to several state-of-the-art methods.</p>","PeriodicalId":94280,"journal":{"name":"Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention","volume":"15002 ","pages":"227-237"},"PeriodicalIF":0.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11513182/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142515737","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Surface-based and Shape-informed U-fiber Atlasing for Robust Superficial White Matter Connectivity Analysis.","authors":"Yuan Li, Xinyu Nie, Jianwei Zhang, Yonggang Shi","doi":"10.1007/978-3-031-72069-7_40","DOIUrl":"10.1007/978-3-031-72069-7_40","url":null,"abstract":"<p><p>Superficial white matter (SWM) U-fibers contain considerable structural connectivity in the human brain; however, related studies are not well-developed compared to the well-studied deep white matter (DWM). Conventionally, SWM U-fiber is obtained through DWM tracking, which is inaccurate on the cortical surface. The significant variability in the cortical folding patterns of the human brain renders a conventional template-based atlas unsuitable for accurately mapping U-fibers within the thin layer of SWM beneath the cortical surface. Recently, new surface-based tracking methods have been developed to reconstruct more complete and reliable U-fibers. To leverage surface-based U-fiber tracking methods, we propose to create a surface-based U-fiber dictionary using high-resolution diffusion MRI (dMRI) data from the Human Connectome Project (HCP). We first identify the major U-fiber bundles and then build a dictionary containing subjects with high groupwise consistency of major U-fiber bundles. Finally, we propose a shape-informed U-fiber atlasing method for robust SWM connectivity analysis. Through experiments, we demonstrate that our shape-informed atlasing method can obtain anatomically more accurate U-fiber representations than state-of-the-art atlas. Additionally, our method is capable of restoring incomplete U-fibers in low-resolution dMRI, thus helping better characterize SWM connectivity in clinical studies such as the Alzheimer's Disease Neuroimaging Initiative (ADNI).</p>","PeriodicalId":94280,"journal":{"name":"Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention","volume":"15002 ","pages":"422-432"},"PeriodicalIF":0.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12448713/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145115740","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Vessel-aware aneurysm detection using multi-scale deformable 3D attention.","authors":"Alberto M Ceballos-Arroyo, Hieu T Nguyen, Fangrui Zhu, Shrikanth M Yadav, Jisoo Kim, Lei Qin, Geoffrey Young, Huaizu Jiang","doi":"10.1007/978-3-031-72086-4_71","DOIUrl":"https://doi.org/10.1007/978-3-031-72086-4_71","url":null,"abstract":"<p><p>Manual detection of intracranial aneurysms (IAs) in computed tomography (CT) scans is a complex, time-consuming task even for expert clinicians, and automating the process is no less challenging. Critical difficulties associated with detecting aneurysms include their small (yet varied) size compared to scans and a high potential for false positive (FP) predictions. To address these issues, we propose a 3D, multi-scale neural architecture that detects aneurysms via a deformable attention mechanism that operates on vessel distance maps derived from vessel segmentations and 3D features extracted from the layers of a convolutional network. Likewise, we reformulate aneurysm segmentation as bounding cuboid prediction using binary cross entropy and three localization losses (location, size, IoU). Given three validation sets comprised of 152/138/38 CT scans and containing 126/101/58 aneurysms, we achieved a Sensitivity of 91.3%/97.0%/74.1% @ FP rates 0.53/0.56/0.87, with Sensitivity around 80% on small aneurysms. Manual inspection of outputs by experts showed our model only tends to miss aneurysms located in unusual locations. Code and model weights are available online.</p>","PeriodicalId":94280,"journal":{"name":"Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention","volume":"15005 ","pages":"754-765"},"PeriodicalIF":0.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11986933/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144013943","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An approach to building foundation models for brain image analysis.","authors":"Davood Karimi","doi":"10.1007/978-3-031-72390-2_40","DOIUrl":"https://doi.org/10.1007/978-3-031-72390-2_40","url":null,"abstract":"<p><p>Existing machine learning methods for brain image analysis are mostly based on supervised training. They require large labeled datasets, which can be costly or impossible to obtain. Moreover, the trained models are useful only for the narrow task defined by the labels. In this work, we developed a new method, based on the concept of foundation models, to overcome these limitations. Our model is an attention-based neural network that is trained using a novel self-supervised approach. Specifically, the model is trained to generate brain images in a patch-wise manner, thereby learning the brain structure. To facilitate learning of image details, we propose a new method that encodes high-frequency information using convolutional kernels with random weights. We trained our model on a pool of 10 public datasets. We then applied the model on five independent datasets to perform segmentation, lesion detection, denoising, and brain age estimation. Results showed that the foundation model achieved competitive or better results on all tasks, while significantly reducing the required amount of labeled training data. Our method enables leveraging large unlabeled neuroimaging datasets to effectively address diverse brain image analysis tasks and reduce the time and cost requirements of acquiring labels.</p>","PeriodicalId":94280,"journal":{"name":"Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention","volume":"15012 ","pages":"421-431"},"PeriodicalIF":0.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12033034/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144048319","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}