Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention最新文献
Pub Date : 2023-06-26DOI: 10.48550/arXiv.2306.14680
Haoran Dou, N. Ravikumar, Alejandro F Frangi
The generation of virtual populations (VPs) of anatomy is essential for conducting in silico trials of medical devices. Typically, the generated VP should capture sufficient variability while remaining plausible and should reflect the specific characteristics and demographics of the patients observed in real populations. In several applications, it is desirable to synthesise virtual populations in a textit{controlled} manner, where relevant covariates are used to conditionally synthesise virtual populations that fit a specific target population/characteristics. We propose to equip a conditional variational autoencoder (cVAE) with normalising flows to boost the flexibility and complexity of the approximate posterior learnt, leading to enhanced flexibility for controllable synthesis of VPs of anatomical structures. We demonstrate the performance of our conditional flow VAE using a data set of cardiac left ventricles acquired from 2360 patients, with associated demographic information and clinical measurements (used as covariates/conditional information). The results obtained indicate the superiority of the proposed method for conditional synthesis of virtual populations of cardiac left ventricles relative to a cVAE. Conditional synthesis performance was evaluated in terms of generalisation and specificity errors and in terms of the ability to preserve clinically relevant biomarkers in synthesised VPs, that is, the left ventricular blood pool and myocardial volume, relative to the real observed population.
{"title":"A Conditional Flow Variational Autoencoder for Controllable Synthesis of Virtual Populations of Anatomy","authors":"Haoran Dou, N. Ravikumar, Alejandro F Frangi","doi":"10.48550/arXiv.2306.14680","DOIUrl":"https://doi.org/10.48550/arXiv.2306.14680","url":null,"abstract":"The generation of virtual populations (VPs) of anatomy is essential for conducting in silico trials of medical devices. Typically, the generated VP should capture sufficient variability while remaining plausible and should reflect the specific characteristics and demographics of the patients observed in real populations. In several applications, it is desirable to synthesise virtual populations in a textit{controlled} manner, where relevant covariates are used to conditionally synthesise virtual populations that fit a specific target population/characteristics. We propose to equip a conditional variational autoencoder (cVAE) with normalising flows to boost the flexibility and complexity of the approximate posterior learnt, leading to enhanced flexibility for controllable synthesis of VPs of anatomical structures. We demonstrate the performance of our conditional flow VAE using a data set of cardiac left ventricles acquired from 2360 patients, with associated demographic information and clinical measurements (used as covariates/conditional information). The results obtained indicate the superiority of the proposed method for conditional synthesis of virtual populations of cardiac left ventricles relative to a cVAE. Conditional synthesis performance was evaluated in terms of generalisation and specificity errors and in terms of the ability to preserve clinically relevant biomarkers in synthesised VPs, that is, the left ventricular blood pool and myocardial volume, relative to the real observed population.","PeriodicalId":18289,"journal":{"name":"Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention","volume":"62 8 1","pages":"143-152"},"PeriodicalIF":0.0,"publicationDate":"2023-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80813124","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-06-26DOI: 10.48550/arXiv.2306.14505
Yu-Jen Chen, Xinrong Hu, Yi Shi, Tsung-Yi Ho
Magnetic resonance imaging (MRI) is commonly used for brain tumor segmentation, which is critical for patient evaluation and treatment planning. To reduce the labor and expertise required for labeling, weakly-supervised semantic segmentation (WSSS) methods with class activation mapping (CAM) have been proposed. However, existing CAM methods suffer from low resolution due to strided convolution and pooling layers, resulting in inaccurate predictions. In this study, we propose a novel CAM method, Attentive Multiple-Exit CAM (AME-CAM), that extracts activation maps from multiple resolutions to hierarchically aggregate and improve prediction accuracy. We evaluate our method on the BraTS 2021 dataset and show that it outperforms state-of-the-art methods.
{"title":"AME-CAM: Attentive Multiple-Exit CAM for Weakly Supervised Segmentation on MRI Brain Tumor","authors":"Yu-Jen Chen, Xinrong Hu, Yi Shi, Tsung-Yi Ho","doi":"10.48550/arXiv.2306.14505","DOIUrl":"https://doi.org/10.48550/arXiv.2306.14505","url":null,"abstract":"Magnetic resonance imaging (MRI) is commonly used for brain tumor segmentation, which is critical for patient evaluation and treatment planning. To reduce the labor and expertise required for labeling, weakly-supervised semantic segmentation (WSSS) methods with class activation mapping (CAM) have been proposed. However, existing CAM methods suffer from low resolution due to strided convolution and pooling layers, resulting in inaccurate predictions. In this study, we propose a novel CAM method, Attentive Multiple-Exit CAM (AME-CAM), that extracts activation maps from multiple resolutions to hierarchically aggregate and improve prediction accuracy. We evaluate our method on the BraTS 2021 dataset and show that it outperforms state-of-the-art methods.","PeriodicalId":18289,"journal":{"name":"Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention","volume":"8 1","pages":"173-182"},"PeriodicalIF":0.0,"publicationDate":"2023-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91025864","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-06-26DOI: 10.48550/arXiv.2306.14638
Faris Almalik, Naif Alkhunaizi, Ibrahim Almakky, K. Nandakumar
Data scarcity is a significant obstacle hindering the learning of powerful machine learning models in critical healthcare applications. Data-sharing mechanisms among multiple entities (e.g., hospitals) can accelerate model training and yield more accurate predictions. Recently, approaches such as Federated Learning (FL) and Split Learning (SL) have facilitated collaboration without the need to exchange private data. In this work, we propose a framework for medical imaging classification tasks called Federated Split learning of Vision transformer with Block Sampling (FeSViBS). The FeSViBS framework builds upon the existing federated split vision transformer and introduces a block sampling module, which leverages intermediate features extracted by the Vision Transformer (ViT) at the server. This is achieved by sampling features (patch tokens) from an intermediate transformer block and distilling their information content into a pseudo class token before passing them back to the client. These pseudo class tokens serve as an effective feature augmentation strategy and enhances the generalizability of the learned model. We demonstrate the utility of our proposed method compared to other SL and FL approaches on three publicly available medical imaging datasets: HAM1000, BloodMNIST, and Fed-ISIC2019, under both IID and non-IID settings. Code: https://github.com/faresmalik/FeSViBS
{"title":"FeSViBS: Federated Split Learning of Vision Transformer with Block Sampling","authors":"Faris Almalik, Naif Alkhunaizi, Ibrahim Almakky, K. Nandakumar","doi":"10.48550/arXiv.2306.14638","DOIUrl":"https://doi.org/10.48550/arXiv.2306.14638","url":null,"abstract":"Data scarcity is a significant obstacle hindering the learning of powerful machine learning models in critical healthcare applications. Data-sharing mechanisms among multiple entities (e.g., hospitals) can accelerate model training and yield more accurate predictions. Recently, approaches such as Federated Learning (FL) and Split Learning (SL) have facilitated collaboration without the need to exchange private data. In this work, we propose a framework for medical imaging classification tasks called Federated Split learning of Vision transformer with Block Sampling (FeSViBS). The FeSViBS framework builds upon the existing federated split vision transformer and introduces a block sampling module, which leverages intermediate features extracted by the Vision Transformer (ViT) at the server. This is achieved by sampling features (patch tokens) from an intermediate transformer block and distilling their information content into a pseudo class token before passing them back to the client. These pseudo class tokens serve as an effective feature augmentation strategy and enhances the generalizability of the learned model. We demonstrate the utility of our proposed method compared to other SL and FL approaches on three publicly available medical imaging datasets: HAM1000, BloodMNIST, and Fed-ISIC2019, under both IID and non-IID settings. Code: https://github.com/faresmalik/FeSViBS","PeriodicalId":18289,"journal":{"name":"Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention","volume":"64 1","pages":"350-360"},"PeriodicalIF":0.0,"publicationDate":"2023-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87463940","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
When deep neural network has been proposed to assist the dentist in designing the location of dental implant, most of them are targeting simple cases where only one missing tooth is available. As a result, literature works do not work well when there are multiple missing teeth and easily generate false predictions when the teeth are sparsely distributed. In this paper, we are trying to integrate a weak supervision text, the target region, to the implant position regression network, to address above issues. We propose a text condition embedded implant position regression network (TCEIP), to embed the text condition into the encoder-decoder framework for improvement of the regression performance. A cross-modal interaction that consists of cross-modal attention (CMA) and knowledge alignment module (KAM) is proposed to facilitate the interaction between features of images and texts. The CMA module performs a cross-attention between the image feature and the text condition, and the KAM mitigates the knowledge gap between the image feature and the image encoder of the CLIP. Extensive experiments on a dental implant dataset through five-fold cross-validation demonstrated that the proposed TCEIP achieves superior performance than existing methods.
{"title":"TCEIP: Text Condition Embedded Regression Network for Dental Implant Position Prediction","authors":"Xinquan Yang, Jinheng Xie, Xuguang Li, Xuechen Li, X. Li, Linlin Shen, Yongqiang Deng","doi":"10.48550/arXiv.2306.14406","DOIUrl":"https://doi.org/10.48550/arXiv.2306.14406","url":null,"abstract":"When deep neural network has been proposed to assist the dentist in designing the location of dental implant, most of them are targeting simple cases where only one missing tooth is available. As a result, literature works do not work well when there are multiple missing teeth and easily generate false predictions when the teeth are sparsely distributed. In this paper, we are trying to integrate a weak supervision text, the target region, to the implant position regression network, to address above issues. We propose a text condition embedded implant position regression network (TCEIP), to embed the text condition into the encoder-decoder framework for improvement of the regression performance. A cross-modal interaction that consists of cross-modal attention (CMA) and knowledge alignment module (KAM) is proposed to facilitate the interaction between features of images and texts. The CMA module performs a cross-attention between the image feature and the text condition, and the KAM mitigates the knowledge gap between the image feature and the image encoder of the CLIP. Extensive experiments on a dental implant dataset through five-fold cross-validation demonstrated that the proposed TCEIP achieves superior performance than existing methods.","PeriodicalId":18289,"journal":{"name":"Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention","volume":"112 1","pages":"317-326"},"PeriodicalIF":0.0,"publicationDate":"2023-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90390230","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-06-26DOI: 10.48550/arXiv.2306.14749
Alexander Bigalke, M. Heinrich
Point cloud-based medical registration promises increased computational efficiency, robustness to intensity shifts, and anonymity preservation but is limited by the inefficacy of unsupervised learning with similarity metrics. Supervised training on synthetic deformations is an alternative but, in turn, suffers from the domain gap to the real domain. In this work, we aim to tackle this gap through domain adaptation. Self-training with the Mean Teacher is an established approach to this problem but is impaired by the inherent noise of the pseudo labels from the teacher. As a remedy, we present a denoised teacher-student paradigm for point cloud registration, comprising two complementary denoising strategies. First, we propose to filter pseudo labels based on the Chamfer distances of teacher and student registrations, thus preventing detrimental supervision by the teacher. Second, we make the teacher dynamically synthesize novel training pairs with noise-free labels by warping its moving inputs with the predicted deformations. Evaluation is performed for inhale-to-exhale registration of lung vessel trees on the public PVT dataset under two domain shifts. Our method surpasses the baseline Mean Teacher by 13.5/62.8%, consistently outperforms diverse competitors, and sets a new state-of-the-art accuracy (TRE=2.31mm). Code is available at https://github.com/multimodallearning/denoised_mt_pcd_reg.
{"title":"A denoised Mean Teacher for domain adaptive point cloud registration","authors":"Alexander Bigalke, M. Heinrich","doi":"10.48550/arXiv.2306.14749","DOIUrl":"https://doi.org/10.48550/arXiv.2306.14749","url":null,"abstract":"Point cloud-based medical registration promises increased computational efficiency, robustness to intensity shifts, and anonymity preservation but is limited by the inefficacy of unsupervised learning with similarity metrics. Supervised training on synthetic deformations is an alternative but, in turn, suffers from the domain gap to the real domain. In this work, we aim to tackle this gap through domain adaptation. Self-training with the Mean Teacher is an established approach to this problem but is impaired by the inherent noise of the pseudo labels from the teacher. As a remedy, we present a denoised teacher-student paradigm for point cloud registration, comprising two complementary denoising strategies. First, we propose to filter pseudo labels based on the Chamfer distances of teacher and student registrations, thus preventing detrimental supervision by the teacher. Second, we make the teacher dynamically synthesize novel training pairs with noise-free labels by warping its moving inputs with the predicted deformations. Evaluation is performed for inhale-to-exhale registration of lung vessel trees on the public PVT dataset under two domain shifts. Our method surpasses the baseline Mean Teacher by 13.5/62.8%, consistently outperforms diverse competitors, and sets a new state-of-the-art accuracy (TRE=2.31mm). Code is available at https://github.com/multimodallearning/denoised_mt_pcd_reg.","PeriodicalId":18289,"journal":{"name":"Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention","volume":"129 1","pages":"666-676"},"PeriodicalIF":0.0,"publicationDate":"2023-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82925660","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-06-26DOI: 10.48550/arXiv.2306.14459
J. Tan, Won-Ki Jeong
Contrastive learning has gained popularity due to its robustness with good feature representation performance. However, cosine distance, the commonly used similarity metric in contrastive learning, is not well suited to represent the distance between two data points, especially on a nonlinear feature manifold. Inspired by manifold learning, we propose a novel extension of contrastive learning that leverages geodesic distance between features as a similarity metric for histopathology whole slide image classification. To reduce the computational overhead in manifold learning, we propose geodesic-distance-based feature clustering for efficient contrastive loss evaluation using prototypes without time-consuming pairwise feature similarity comparison. The efficacy of the proposed method is evaluated on two real-world histopathology image datasets. Results demonstrate that our method outperforms state-of-the-art cosine-distance-based contrastive learning methods.
{"title":"Histopathology Image Classification using Deep Manifold Contrastive Learning","authors":"J. Tan, Won-Ki Jeong","doi":"10.48550/arXiv.2306.14459","DOIUrl":"https://doi.org/10.48550/arXiv.2306.14459","url":null,"abstract":"Contrastive learning has gained popularity due to its robustness with good feature representation performance. However, cosine distance, the commonly used similarity metric in contrastive learning, is not well suited to represent the distance between two data points, especially on a nonlinear feature manifold. Inspired by manifold learning, we propose a novel extension of contrastive learning that leverages geodesic distance between features as a similarity metric for histopathology whole slide image classification. To reduce the computational overhead in manifold learning, we propose geodesic-distance-based feature clustering for efficient contrastive loss evaluation using prototypes without time-consuming pairwise feature similarity comparison. The efficacy of the proposed method is evaluated on two real-world histopathology image datasets. Results demonstrate that our method outperforms state-of-the-art cosine-distance-based contrastive learning methods.","PeriodicalId":18289,"journal":{"name":"Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention","volume":"30 1","pages":"683-692"},"PeriodicalIF":0.0,"publicationDate":"2023-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76653705","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-06-25DOI: 10.48550/arXiv.2306.14350
Jiahao Huang, Angelica I. Avilés-Rivero, C. Schönlieb, Guang Yang
Deep learning has shown the capability to substantially accelerate MRI reconstruction while acquiring fewer measurements. Recently, diffusion models have gained burgeoning interests as a novel group of deep learning-based generative methods. These methods seek to sample data points that belong to a target distribution from a Gaussian distribution, which has been successfully extended to MRI reconstruction. In this work, we proposed a Cold Diffusion-based MRI reconstruction method called CDiffMR. Different from conventional diffusion models, the degradation operation of our CDiffMR is based on textit{k}-space undersampling instead of adding Gaussian noise, and the restoration network is trained to harness a de-aliaseing function. We also design starting point and data consistency conditioning strategies to guide and accelerate the reverse process. More intriguingly, the pre-trained CDiffMR model can be reused for reconstruction tasks with different undersampling rates. We demonstrated, through extensive numerical and visual experiments, that the proposed CDiffMR can achieve comparable or even superior reconstruction results than state-of-the-art models. Compared to the diffusion model-based counterpart, CDiffMR reaches readily competing results using only $1.6 sim 3.4%$ for inference time. The code is publicly available at https://github.com/ayanglab/CDiffMR.
{"title":"CDiffMR: Can We Replace the Gaussian Noise with K-Space Undersampling for Fast MRI?","authors":"Jiahao Huang, Angelica I. Avilés-Rivero, C. Schönlieb, Guang Yang","doi":"10.48550/arXiv.2306.14350","DOIUrl":"https://doi.org/10.48550/arXiv.2306.14350","url":null,"abstract":"Deep learning has shown the capability to substantially accelerate MRI reconstruction while acquiring fewer measurements. Recently, diffusion models have gained burgeoning interests as a novel group of deep learning-based generative methods. These methods seek to sample data points that belong to a target distribution from a Gaussian distribution, which has been successfully extended to MRI reconstruction. In this work, we proposed a Cold Diffusion-based MRI reconstruction method called CDiffMR. Different from conventional diffusion models, the degradation operation of our CDiffMR is based on textit{k}-space undersampling instead of adding Gaussian noise, and the restoration network is trained to harness a de-aliaseing function. We also design starting point and data consistency conditioning strategies to guide and accelerate the reverse process. More intriguingly, the pre-trained CDiffMR model can be reused for reconstruction tasks with different undersampling rates. We demonstrated, through extensive numerical and visual experiments, that the proposed CDiffMR can achieve comparable or even superior reconstruction results than state-of-the-art models. Compared to the diffusion model-based counterpart, CDiffMR reaches readily competing results using only $1.6 sim 3.4%$ for inference time. The code is publicly available at https://github.com/ayanglab/CDiffMR.","PeriodicalId":18289,"journal":{"name":"Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention","volume":"10 1","pages":"3-12"},"PeriodicalIF":0.0,"publicationDate":"2023-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79174098","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-06-24DOI: 10.48550/arXiv.2306.13960
T. Kuipers, E. Bekkers
Regular group convolutional neural networks (G-CNNs) have been shown to increase model performance and improve equivariance to different geometrical symmetries. This work addresses the problem of SE(3), i.e., roto-translation equivariance, on volumetric data. Volumetric image data is prevalent in many medical settings. Motivated by the recent work on separable group convolutions, we devise a SE(3) group convolution kernel separated into a continuous SO(3) (rotation) kernel and a spatial kernel. We approximate equivariance to the continuous setting by sampling uniform SO(3) grids. Our continuous SO(3) kernel is parameterized via RBF interpolation on similarly uniform grids. We demonstrate the advantages of our approach in volumetric medical image analysis. Our SE(3) equivariant models consistently outperform CNNs and regular discrete G-CNNs on challenging medical classification tasks and show significantly improved generalization capabilities. Our approach achieves up to a 16.5% gain in accuracy over regular CNNs.
{"title":"Regular SE(3) Group Convolutions for Volumetric Medical Image Analysis","authors":"T. Kuipers, E. Bekkers","doi":"10.48550/arXiv.2306.13960","DOIUrl":"https://doi.org/10.48550/arXiv.2306.13960","url":null,"abstract":"Regular group convolutional neural networks (G-CNNs) have been shown to increase model performance and improve equivariance to different geometrical symmetries. This work addresses the problem of SE(3), i.e., roto-translation equivariance, on volumetric data. Volumetric image data is prevalent in many medical settings. Motivated by the recent work on separable group convolutions, we devise a SE(3) group convolution kernel separated into a continuous SO(3) (rotation) kernel and a spatial kernel. We approximate equivariance to the continuous setting by sampling uniform SO(3) grids. Our continuous SO(3) kernel is parameterized via RBF interpolation on similarly uniform grids. We demonstrate the advantages of our approach in volumetric medical image analysis. Our SE(3) equivariant models consistently outperform CNNs and regular discrete G-CNNs on challenging medical classification tasks and show significantly improved generalization capabilities. Our approach achieves up to a 16.5% gain in accuracy over regular CNNs.","PeriodicalId":18289,"journal":{"name":"Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention","volume":"33 1","pages":"252-261"},"PeriodicalIF":0.0,"publicationDate":"2023-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79090356","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Three-dimensional microscopy is often limited by anisotropic spatial resolution, resulting in lower axial resolution than lateral resolution. Current State-of-The-Art (SoTA) isotropic reconstruction methods utilizing deep neural networks can achieve impressive super-resolution performance in fixed imaging settings. However, their generality in practical use is limited by degraded performance caused by artifacts and blurring when facing unseen anisotropic factors. To address these issues, we propose DiffuseIR, an unsupervised method for isotropic reconstruction based on diffusion models. First, we pre-train a diffusion model to learn the structural distribution of biological tissue from lateral microscopic images, resulting in generating naturally high-resolution images. Then we use low-axial-resolution microscopy images to condition the generation process of the diffusion model and generate high-axial-resolution reconstruction results. Since the diffusion model learns the universal structural distribution of biological tissues, which is independent of the axial resolution, DiffuseIR can reconstruct authentic images with unseen low-axial resolutions into a high-axial resolution without requiring re-training. The proposed DiffuseIR achieves SoTA performance in experiments on EM data and can even compete with supervised methods.
{"title":"DiffuseIR: Diffusion Models For Isotropic Reconstruction of 3D Microscopic Images","authors":"Mingjie Pan, Yulu Gan, Fangxu Zhou, Jiaming Liu, Aimin Wang, Shanghang Zhang, Dawei Li","doi":"10.48550/arXiv.2306.12109","DOIUrl":"https://doi.org/10.48550/arXiv.2306.12109","url":null,"abstract":"Three-dimensional microscopy is often limited by anisotropic spatial resolution, resulting in lower axial resolution than lateral resolution. Current State-of-The-Art (SoTA) isotropic reconstruction methods utilizing deep neural networks can achieve impressive super-resolution performance in fixed imaging settings. However, their generality in practical use is limited by degraded performance caused by artifacts and blurring when facing unseen anisotropic factors. To address these issues, we propose DiffuseIR, an unsupervised method for isotropic reconstruction based on diffusion models. First, we pre-train a diffusion model to learn the structural distribution of biological tissue from lateral microscopic images, resulting in generating naturally high-resolution images. Then we use low-axial-resolution microscopy images to condition the generation process of the diffusion model and generate high-axial-resolution reconstruction results. Since the diffusion model learns the universal structural distribution of biological tissues, which is independent of the axial resolution, DiffuseIR can reconstruct authentic images with unseen low-axial resolutions into a high-axial resolution without requiring re-training. The proposed DiffuseIR achieves SoTA performance in experiments on EM data and can even compete with supervised methods.","PeriodicalId":18289,"journal":{"name":"Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention","volume":"14 1","pages":"323-332"},"PeriodicalIF":0.0,"publicationDate":"2023-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89778535","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Staging of liver fibrosis is important in the diagnosis and treatment planning of patients suffering from liver diseases. Current deep learning-based methods using abdominal magnetic resonance imaging (MRI) usually take a sub-region of the liver as an input, which nevertheless could miss critical information. To explore richer representations, we formulate this task as a multi-view learning problem and employ multiple sub-regions of the liver. Previously, features or predictions are usually combined in an implicit manner, and uncertainty-aware methods have been proposed. However, these methods could be challenged to capture cross-view representations, which can be important in the accurate prediction of staging. Therefore, we propose a reliable multi-view learning method with interpretable combination rules, which can model global representations to improve the accuracy of predictions. Specifically, the proposed method estimates uncertainties based on subjective logic to improve reliability, and an explicit combination rule is applied based on Dempster-Shafer's evidence theory with good power of interpretability. Moreover, a data-efficient transformer is introduced to capture representations in the global view. Results evaluated on enhanced MRI data show that our method delivers superior performance over existing multi-view learning methods.
{"title":"A Reliable and Interpretable Framework of Multi-view Learning for Liver Fibrosis Staging","authors":"Zheyao Gao, Yuanye Liu, Fuping Wu, N. Shi, Yuxin Shi, X. Zhuang","doi":"10.48550/arXiv.2306.12054","DOIUrl":"https://doi.org/10.48550/arXiv.2306.12054","url":null,"abstract":"Staging of liver fibrosis is important in the diagnosis and treatment planning of patients suffering from liver diseases. Current deep learning-based methods using abdominal magnetic resonance imaging (MRI) usually take a sub-region of the liver as an input, which nevertheless could miss critical information. To explore richer representations, we formulate this task as a multi-view learning problem and employ multiple sub-regions of the liver. Previously, features or predictions are usually combined in an implicit manner, and uncertainty-aware methods have been proposed. However, these methods could be challenged to capture cross-view representations, which can be important in the accurate prediction of staging. Therefore, we propose a reliable multi-view learning method with interpretable combination rules, which can model global representations to improve the accuracy of predictions. Specifically, the proposed method estimates uncertainties based on subjective logic to improve reliability, and an explicit combination rule is applied based on Dempster-Shafer's evidence theory with good power of interpretability. Moreover, a data-efficient transformer is introduced to capture representations in the global view. Results evaluated on enhanced MRI data show that our method delivers superior performance over existing multi-view learning methods.","PeriodicalId":18289,"journal":{"name":"Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention","volume":"16 1","pages":"178-188"},"PeriodicalIF":0.0,"publicationDate":"2023-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77486057","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention
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