Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention最新文献
Pub Date : 2023-07-17DOI: 10.48550/arXiv.2307.08473
Jiacheng Ruan, Mingye Xie, Jingsheng Gao, Ting Liu, Yuzhuo Fu
Transformer and its variants have been widely used for medical image segmentation. However, the large number of parameter and computational load of these models make them unsuitable for mobile health applications. To address this issue, we propose a more efficient approach, the Efficient Group Enhanced UNet (EGE-UNet). We incorporate a Group multi-axis Hadamard Product Attention module (GHPA) and a Group Aggregation Bridge module (GAB) in a lightweight manner. The GHPA groups input features and performs Hadamard Product Attention mechanism (HPA) on different axes to extract pathological information from diverse perspectives. The GAB effectively fuses multi-scale information by grouping low-level features, high-level features, and a mask generated by the decoder at each stage. Comprehensive experiments on the ISIC2017 and ISIC2018 datasets demonstrate that EGE-UNet outperforms existing state-of-the-art methods. In short, compared to the TransFuse, our model achieves superior segmentation performance while reducing parameter and computation costs by 494x and 160x, respectively. Moreover, to our best knowledge, this is the first model with a parameter count limited to just 50KB. Our code is available at https://github.com/JCruan519/EGE-UNet.
{"title":"EGE-UNet: an Efficient Group Enhanced UNet for skin lesion segmentation","authors":"Jiacheng Ruan, Mingye Xie, Jingsheng Gao, Ting Liu, Yuzhuo Fu","doi":"10.48550/arXiv.2307.08473","DOIUrl":"https://doi.org/10.48550/arXiv.2307.08473","url":null,"abstract":"Transformer and its variants have been widely used for medical image segmentation. However, the large number of parameter and computational load of these models make them unsuitable for mobile health applications. To address this issue, we propose a more efficient approach, the Efficient Group Enhanced UNet (EGE-UNet). We incorporate a Group multi-axis Hadamard Product Attention module (GHPA) and a Group Aggregation Bridge module (GAB) in a lightweight manner. The GHPA groups input features and performs Hadamard Product Attention mechanism (HPA) on different axes to extract pathological information from diverse perspectives. The GAB effectively fuses multi-scale information by grouping low-level features, high-level features, and a mask generated by the decoder at each stage. Comprehensive experiments on the ISIC2017 and ISIC2018 datasets demonstrate that EGE-UNet outperforms existing state-of-the-art methods. In short, compared to the TransFuse, our model achieves superior segmentation performance while reducing parameter and computation costs by 494x and 160x, respectively. Moreover, to our best knowledge, this is the first model with a parameter count limited to just 50KB. Our code is available at https://github.com/JCruan519/EGE-UNet.","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":"481-490"},"PeriodicalIF":0.0,"publicationDate":"2023-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83414833","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 : 2023-07-16DOI: 10.48550/arXiv.2307.07998
Tomás Chobola, Gesine Müller, V. Dausmann, Anton Theileis, J. Taucher, J. Huisken, Tingying Peng
The process of acquiring microscopic images in life sciences often results in image degradation and corruption, characterised by the presence of noise and blur, which poses significant challenges in accurately analysing and interpreting the obtained data. This paper proposes LUCYD, a novel method for the restoration of volumetric microscopy images that combines the Richardson-Lucy deconvolution formula and the fusion of deep features obtained by a fully convolutional network. By integrating the image formation process into a feature-driven restoration model, the proposed approach aims to enhance the quality of the restored images whilst reducing computational costs and maintaining a high degree of interpretability. Our results demonstrate that LUCYD outperforms the state-of-the-art methods in both synthetic and real microscopy images, achieving superior performance in terms of image quality and generalisability. We show that the model can handle various microscopy modalities and different imaging conditions by evaluating it on two different microscopy datasets, including volumetric widefield and light-sheet microscopy. Our experiments indicate that LUCYD can significantly improve resolution, contrast, and overall quality of microscopy images. Therefore, it can be a valuable tool for microscopy image restoration and can facilitate further research in various microscopy applications. We made the source code for the model accessible under https://github.com/ctom2/lucyd-deconvolution.
{"title":"LUCYD: A Feature-Driven Richardson-Lucy Deconvolution Network","authors":"Tomás Chobola, Gesine Müller, V. Dausmann, Anton Theileis, J. Taucher, J. Huisken, Tingying Peng","doi":"10.48550/arXiv.2307.07998","DOIUrl":"https://doi.org/10.48550/arXiv.2307.07998","url":null,"abstract":"The process of acquiring microscopic images in life sciences often results in image degradation and corruption, characterised by the presence of noise and blur, which poses significant challenges in accurately analysing and interpreting the obtained data. This paper proposes LUCYD, a novel method for the restoration of volumetric microscopy images that combines the Richardson-Lucy deconvolution formula and the fusion of deep features obtained by a fully convolutional network. By integrating the image formation process into a feature-driven restoration model, the proposed approach aims to enhance the quality of the restored images whilst reducing computational costs and maintaining a high degree of interpretability. Our results demonstrate that LUCYD outperforms the state-of-the-art methods in both synthetic and real microscopy images, achieving superior performance in terms of image quality and generalisability. We show that the model can handle various microscopy modalities and different imaging conditions by evaluating it on two different microscopy datasets, including volumetric widefield and light-sheet microscopy. Our experiments indicate that LUCYD can significantly improve resolution, contrast, and overall quality of microscopy images. Therefore, it can be a valuable tool for microscopy image restoration and can facilitate further research in various microscopy applications. We made the source code for the model accessible under https://github.com/ctom2/lucyd-deconvolution.","PeriodicalId":18289,"journal":{"name":"Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention","volume":"55 27 1","pages":"656-665"},"PeriodicalIF":0.0,"publicationDate":"2023-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88488510","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 : 2023-07-14DOI: 10.48550/arXiv.2307.07168
Jingna Qiu, Frauke Wilm, Mathias Öttl, M. Schlereth, Chang Liu, T. Heimann, M. Aubreville, K. Breininger
The process of annotating histological gigapixel-sized whole slide images (WSIs) at the pixel level for the purpose of training a supervised segmentation model is time-consuming. Region-based active learning (AL) involves training the model on a limited number of annotated image regions instead of requesting annotations of the entire images. These annotation regions are iteratively selected, with the goal of optimizing model performance while minimizing the annotated area. The standard method for region selection evaluates the informativeness of all square regions of a specified size and then selects a specific quantity of the most informative regions. We find that the efficiency of this method highly depends on the choice of AL step size (i.e., the combination of region size and the number of selected regions per WSI), and a suboptimal AL step size can result in redundant annotation requests or inflated computation costs. This paper introduces a novel technique for selecting annotation regions adaptively, mitigating the reliance on this AL hyperparameter. Specifically, we dynamically determine each region by first identifying an informative area and then detecting its optimal bounding box, as opposed to selecting regions of a uniform predefined shape and size as in the standard method. We evaluate our method using the task of breast cancer metastases segmentation on the public CAMELYON16 dataset and show that it consistently achieves higher sampling efficiency than the standard method across various AL step sizes. With only 2.6% of tissue area annotated, we achieve full annotation performance and thereby substantially reduce the costs of annotating a WSI dataset. The source code is available at https://github.com/DeepMicroscopy/AdaptiveRegionSelection.
{"title":"Adaptive Region Selection for Active Learning in Whole Slide Image Semantic Segmentation","authors":"Jingna Qiu, Frauke Wilm, Mathias Öttl, M. Schlereth, Chang Liu, T. Heimann, M. Aubreville, K. Breininger","doi":"10.48550/arXiv.2307.07168","DOIUrl":"https://doi.org/10.48550/arXiv.2307.07168","url":null,"abstract":"The process of annotating histological gigapixel-sized whole slide images (WSIs) at the pixel level for the purpose of training a supervised segmentation model is time-consuming. Region-based active learning (AL) involves training the model on a limited number of annotated image regions instead of requesting annotations of the entire images. These annotation regions are iteratively selected, with the goal of optimizing model performance while minimizing the annotated area. The standard method for region selection evaluates the informativeness of all square regions of a specified size and then selects a specific quantity of the most informative regions. We find that the efficiency of this method highly depends on the choice of AL step size (i.e., the combination of region size and the number of selected regions per WSI), and a suboptimal AL step size can result in redundant annotation requests or inflated computation costs. This paper introduces a novel technique for selecting annotation regions adaptively, mitigating the reliance on this AL hyperparameter. Specifically, we dynamically determine each region by first identifying an informative area and then detecting its optimal bounding box, as opposed to selecting regions of a uniform predefined shape and size as in the standard method. We evaluate our method using the task of breast cancer metastases segmentation on the public CAMELYON16 dataset and show that it consistently achieves higher sampling efficiency than the standard method across various AL step sizes. With only 2.6% of tissue area annotated, we achieve full annotation performance and thereby substantially reduce the costs of annotating a WSI dataset. The source code is available at https://github.com/DeepMicroscopy/AdaptiveRegionSelection.","PeriodicalId":18289,"journal":{"name":"Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention","volume":"74 1","pages":"90-100"},"PeriodicalIF":0.0,"publicationDate":"2023-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72933758","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 : 2023-07-14DOI: 10.48550/arXiv.2307.07254
Sílvia D. Almeida, Carsten T. Lüth, T. Norajitra, T. Wald, M. Nolden, P. Jaeger, C. Heussel, J. Biederer, O. Weinheimer, K. Maier-Hein
Classification of heterogeneous diseases is challenging due to their complexity, variability of symptoms and imaging findings. Chronic Obstructive Pulmonary Disease (COPD) is a prime example, being underdiagnosed despite being the third leading cause of death. Its sparse, diffuse and heterogeneous appearance on computed tomography challenges supervised binary classification. We reformulate COPD binary classification as an anomaly detection task, proposing cOOpD: heterogeneous pathological regions are detected as Out-of-Distribution (OOD) from normal homogeneous lung regions. To this end, we learn representations of unlabeled lung regions employing a self-supervised contrastive pretext model, potentially capturing specific characteristics of diseased and healthy unlabeled regions. A generative model then learns the distribution of healthy representations and identifies abnormalities (stemming from COPD) as deviations. Patient-level scores are obtained by aggregating region OOD scores. We show that cOOpD achieves the best performance on two public datasets, with an increase of 8.2% and 7.7% in terms of AUROC compared to the previous supervised state-of-the-art. Additionally, cOOpD yields well-interpretable spatial anomaly maps and patient-level scores which we show to be of additional value in identifying individuals in the early stage of progression. Experiments in artificially designed real-world prevalence settings further support that anomaly detection is a powerful way of tackling COPD classification.
异质性疾病的分类是具有挑战性的，由于其复杂性，变异性的症状和影像学表现。慢性阻塞性肺疾病(COPD)就是一个典型的例子，尽管它是第三大死亡原因，但仍未得到充分诊断。它在计算机断层扫描上的稀疏、弥散和异质性表现对监督二分类提出了挑战。我们将COPD二元分类重新定义为异常检测任务，提出COPD:异质性病理区域被检测为来自正常均匀肺区域的out - distribution (OOD)。为此，我们使用自我监督对比借口模型学习未标记肺区域的表示，潜在地捕获患病和健康未标记区域的特定特征。然后生成模型学习健康表征的分布，并将异常(源于COPD)识别为偏差。患者水平评分是通过汇总地区OOD评分获得的。我们表明，cOOpD在两个公共数据集上实现了最佳性能，与之前的监督技术相比，在AUROC方面增加了8.2%和7.7%。此外，cOOpD产生了可很好解释的空间异常图和患者水平评分，我们认为这在识别早期进展阶段的个体方面具有附加价值。在人为设计的真实世界患病率环境中进行的实验进一步支持异常检测是解决COPD分类的有力方法。
{"title":"cOOpD: Reformulating COPD classification on chest CT scans as anomaly detection using contrastive representations","authors":"Sílvia D. Almeida, Carsten T. Lüth, T. Norajitra, T. Wald, M. Nolden, P. Jaeger, C. Heussel, J. Biederer, O. Weinheimer, K. Maier-Hein","doi":"10.48550/arXiv.2307.07254","DOIUrl":"https://doi.org/10.48550/arXiv.2307.07254","url":null,"abstract":"Classification of heterogeneous diseases is challenging due to their complexity, variability of symptoms and imaging findings. Chronic Obstructive Pulmonary Disease (COPD) is a prime example, being underdiagnosed despite being the third leading cause of death. Its sparse, diffuse and heterogeneous appearance on computed tomography challenges supervised binary classification. We reformulate COPD binary classification as an anomaly detection task, proposing cOOpD: heterogeneous pathological regions are detected as Out-of-Distribution (OOD) from normal homogeneous lung regions. To this end, we learn representations of unlabeled lung regions employing a self-supervised contrastive pretext model, potentially capturing specific characteristics of diseased and healthy unlabeled regions. A generative model then learns the distribution of healthy representations and identifies abnormalities (stemming from COPD) as deviations. Patient-level scores are obtained by aggregating region OOD scores. We show that cOOpD achieves the best performance on two public datasets, with an increase of 8.2% and 7.7% in terms of AUROC compared to the previous supervised state-of-the-art. Additionally, cOOpD yields well-interpretable spatial anomaly maps and patient-level scores which we show to be of additional value in identifying individuals in the early stage of progression. Experiments in artificially designed real-world prevalence settings further support that anomaly detection is a powerful way of tackling COPD classification.","PeriodicalId":18289,"journal":{"name":"Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention","volume":"20 1","pages":"33-43"},"PeriodicalIF":0.0,"publicationDate":"2023-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81699235","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 : 2023-07-14DOI: 10.48550/arXiv.2307.07541
Marc Demoustier, Yue Zhang, V. N. Murthy, Florin C. Ghesu, D. Comaniciu
Device tracking is an important prerequisite for guidance during endovascular procedures. Especially during cardiac interventions, detection and tracking of guiding the catheter tip in 2D fluoroscopic images is important for applications such as mapping vessels from angiography (high dose with contrast) to fluoroscopy (low dose without contrast). Tracking the catheter tip poses different challenges: the tip can be occluded by contrast during angiography or interventional devices; and it is always in continuous movement due to the cardiac and respiratory motions. To overcome these challenges, we propose ConTrack, a transformer-based network that uses both spatial and temporal contextual information for accurate device detection and tracking in both X-ray fluoroscopy and angiography. The spatial information comes from the template frames and the segmentation module: the template frames define the surroundings of the device, whereas the segmentation module detects the entire device to bring more context for the tip prediction. Using multiple templates makes the model more robust to the change in appearance of the device when it is occluded by the contrast agent. The flow information computed on the segmented catheter mask between the current and the previous frame helps in further refining the prediction by compensating for the respiratory and cardiac motions. The experiments show that our method achieves 45% or higher accuracy in detection and tracking when compared to state-of-the-art tracking models.
{"title":"ConTrack: Contextual Transformer for Device Tracking in X-ray","authors":"Marc Demoustier, Yue Zhang, V. N. Murthy, Florin C. Ghesu, D. Comaniciu","doi":"10.48550/arXiv.2307.07541","DOIUrl":"https://doi.org/10.48550/arXiv.2307.07541","url":null,"abstract":"Device tracking is an important prerequisite for guidance during endovascular procedures. Especially during cardiac interventions, detection and tracking of guiding the catheter tip in 2D fluoroscopic images is important for applications such as mapping vessels from angiography (high dose with contrast) to fluoroscopy (low dose without contrast). Tracking the catheter tip poses different challenges: the tip can be occluded by contrast during angiography or interventional devices; and it is always in continuous movement due to the cardiac and respiratory motions. To overcome these challenges, we propose ConTrack, a transformer-based network that uses both spatial and temporal contextual information for accurate device detection and tracking in both X-ray fluoroscopy and angiography. The spatial information comes from the template frames and the segmentation module: the template frames define the surroundings of the device, whereas the segmentation module detects the entire device to bring more context for the tip prediction. Using multiple templates makes the model more robust to the change in appearance of the device when it is occluded by the contrast agent. The flow information computed on the segmented catheter mask between the current and the previous frame helps in further refining the prediction by compensating for the respiratory and cardiac motions. The experiments show that our method achieves 45% or higher accuracy in detection and tracking when compared to state-of-the-art tracking models.","PeriodicalId":18289,"journal":{"name":"Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention","volume":"44 1","pages":"679-688"},"PeriodicalIF":0.0,"publicationDate":"2023-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76704601","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 : 2023-07-14DOI: 10.48550/arXiv.2307.09973
Longxiang Tang, Kai Li, Chunming He, Yulun Zhang, Xiu Li
This paper studies source-free domain adaptive fundus image segmentation which aims to adapt a pretrained fundus segmentation model to a target domain using unlabeled images. This is a challenging task because it is highly risky to adapt a model only using unlabeled data. Most existing methods tackle this task mainly by designing techniques to carefully generate pseudo labels from the model's predictions and use the pseudo labels to train the model. While often obtaining positive adaption effects, these methods suffer from two major issues. First, they tend to be fairly unstable - incorrect pseudo labels abruptly emerged may cause a catastrophic impact on the model. Second, they fail to consider the severe class imbalance of fundus images where the foreground (e.g., cup) region is usually very small. This paper aims to address these two issues by proposing the Class-Balanced Mean Teacher (CBMT) model. CBMT addresses the unstable issue by proposing a weak-strong augmented mean teacher learning scheme where only the teacher model generates pseudo labels from weakly augmented images to train a student model that takes strongly augmented images as input. The teacher is updated as the moving average of the instantly trained student, which could be noisy. This prevents the teacher model from being abruptly impacted by incorrect pseudo-labels. For the class imbalance issue, CBMT proposes a novel loss calibration approach to highlight foreground classes according to global statistics. Experiments show that CBMT well addresses these two issues and outperforms existing methods on multiple benchmarks.
{"title":"Source-Free Domain Adaptive Fundus Image Segmentation with Class-Balanced Mean Teacher","authors":"Longxiang Tang, Kai Li, Chunming He, Yulun Zhang, Xiu Li","doi":"10.48550/arXiv.2307.09973","DOIUrl":"https://doi.org/10.48550/arXiv.2307.09973","url":null,"abstract":"This paper studies source-free domain adaptive fundus image segmentation which aims to adapt a pretrained fundus segmentation model to a target domain using unlabeled images. This is a challenging task because it is highly risky to adapt a model only using unlabeled data. Most existing methods tackle this task mainly by designing techniques to carefully generate pseudo labels from the model's predictions and use the pseudo labels to train the model. While often obtaining positive adaption effects, these methods suffer from two major issues. First, they tend to be fairly unstable - incorrect pseudo labels abruptly emerged may cause a catastrophic impact on the model. Second, they fail to consider the severe class imbalance of fundus images where the foreground (e.g., cup) region is usually very small. This paper aims to address these two issues by proposing the Class-Balanced Mean Teacher (CBMT) model. CBMT addresses the unstable issue by proposing a weak-strong augmented mean teacher learning scheme where only the teacher model generates pseudo labels from weakly augmented images to train a student model that takes strongly augmented images as input. The teacher is updated as the moving average of the instantly trained student, which could be noisy. This prevents the teacher model from being abruptly impacted by incorrect pseudo-labels. For the class imbalance issue, CBMT proposes a novel loss calibration approach to highlight foreground classes according to global statistics. Experiments show that CBMT well addresses these two issues and outperforms existing methods on multiple benchmarks.","PeriodicalId":18289,"journal":{"name":"Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention","volume":"191 1","pages":"684-694"},"PeriodicalIF":0.0,"publicationDate":"2023-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74780102","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 : 2023-07-13DOI: 10.48550/arXiv.2307.06666
Marzieh Oghbaie, Teresa Araújo, T. Emre, U. Schmidt-Erfurth, H. Bogunović
The automatic classification of 3D medical data is memory-intensive. Also, variations in the number of slices between samples is common. Na"ive solutions such as subsampling can solve these problems, but at the cost of potentially eliminating relevant diagnosis information. Transformers have shown promising performance for sequential data analysis. However, their application for long sequences is data, computationally, and memory demanding. In this paper, we propose an end-to-end Transformer-based framework that allows to classify volumetric data of variable length in an efficient fashion. Particularly, by randomizing the input volume-wise resolution(#slices) during training, we enhance the capacity of the learnable positional embedding assigned to each volume slice. Consequently, the accumulated positional information in each positional embedding can be generalized to the neighbouring slices, even for high-resolution volumes at the test time. By doing so, the model will be more robust to variable volume length and amenable to different computational budgets. We evaluated the proposed approach in retinal OCT volume classification and achieved 21.96% average improvement in balanced accuracy on a 9-class diagnostic task, compared to state-of-the-art video transformers. Our findings show that varying the volume-wise resolution of the input during training results in more informative volume representation as compared to training with fixed number of slices per volume.
{"title":"Transformer-based end-to-end classification of variable-length volumetric data","authors":"Marzieh Oghbaie, Teresa Araújo, T. Emre, U. Schmidt-Erfurth, H. Bogunović","doi":"10.48550/arXiv.2307.06666","DOIUrl":"https://doi.org/10.48550/arXiv.2307.06666","url":null,"abstract":"The automatic classification of 3D medical data is memory-intensive. Also, variations in the number of slices between samples is common. Na\"ive solutions such as subsampling can solve these problems, but at the cost of potentially eliminating relevant diagnosis information. Transformers have shown promising performance for sequential data analysis. However, their application for long sequences is data, computationally, and memory demanding. In this paper, we propose an end-to-end Transformer-based framework that allows to classify volumetric data of variable length in an efficient fashion. Particularly, by randomizing the input volume-wise resolution(#slices) during training, we enhance the capacity of the learnable positional embedding assigned to each volume slice. Consequently, the accumulated positional information in each positional embedding can be generalized to the neighbouring slices, even for high-resolution volumes at the test time. By doing so, the model will be more robust to variable volume length and amenable to different computational budgets. We evaluated the proposed approach in retinal OCT volume classification and achieved 21.96% average improvement in balanced accuracy on a 9-class diagnostic task, compared to state-of-the-art video transformers. Our findings show that varying the volume-wise resolution of the input during training results in more informative volume representation as compared to training with fixed number of slices per volume.","PeriodicalId":18289,"journal":{"name":"Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention","volume":"75 1","pages":"358-367"},"PeriodicalIF":0.0,"publicationDate":"2023-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72819394","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 : 2023-07-12DOI: 10.48550/arXiv.2307.06182
Zhenrong Shen, Mao-Hong Cao, Sheng Wang, Lichi Zhang, Qian Wang
Automatic examination of thin-prep cytologic test (TCT) slides can assist pathologists in finding cervical abnormality for accurate and efficient cancer screening. Current solutions mostly need to localize suspicious cells and classify abnormality based on local patches, concerning the fact that whole slide images of TCT are extremely large. It thus requires many annotations of normal and abnormal cervical cells, to supervise the training of the patch-level classifier for promising performance. In this paper, we propose CellGAN to synthesize cytopathological images of various cervical cell types for augmenting patch-level cell classification. Built upon a lightweight backbone, CellGAN is equipped with a non-linear class mapping network to effectively incorporate cell type information into image generation. We also propose the Skip-layer Global Context module to model the complex spatial relationship of the cells, and attain high fidelity of the synthesized images through adversarial learning. Our experiments demonstrate that CellGAN can produce visually plausible TCT cytopathological images for different cell types. We also validate the effectiveness of using CellGAN to greatly augment patch-level cell classification performance.
自动检查薄层细胞学检查(TCT)玻片可以帮助病理学家发现宫颈异常准确和有效的癌症筛查。目前的解决方案大多需要定位可疑细胞，并基于局部斑块对异常进行分类，因为TCT的整个幻灯片图像非常大。因此，它需要对正常和异常的宫颈细胞进行许多注释，以监督补丁级分类器的训练，以获得有希望的性能。在本文中，我们提出CellGAN来合成各种宫颈细胞类型的细胞病理图像，以增强斑块水平的细胞分类。CellGAN基于轻量级主干，配备非线性类映射网络，有效地将细胞类型信息整合到图像生成中。我们还提出了Skip-layer Global Context模块来模拟细胞之间复杂的空间关系，并通过对抗性学习来获得高保真的合成图像。我们的实验表明，CellGAN可以为不同的细胞类型产生视觉上可信的TCT细胞病理图像。我们还验证了使用CellGAN大大增强斑块级细胞分类性能的有效性。
{"title":"CellGAN: Conditional Cervical Cell Synthesis for Augmenting Cytopathological Image Classification","authors":"Zhenrong Shen, Mao-Hong Cao, Sheng Wang, Lichi Zhang, Qian Wang","doi":"10.48550/arXiv.2307.06182","DOIUrl":"https://doi.org/10.48550/arXiv.2307.06182","url":null,"abstract":"Automatic examination of thin-prep cytologic test (TCT) slides can assist pathologists in finding cervical abnormality for accurate and efficient cancer screening. Current solutions mostly need to localize suspicious cells and classify abnormality based on local patches, concerning the fact that whole slide images of TCT are extremely large. It thus requires many annotations of normal and abnormal cervical cells, to supervise the training of the patch-level classifier for promising performance. In this paper, we propose CellGAN to synthesize cytopathological images of various cervical cell types for augmenting patch-level cell classification. Built upon a lightweight backbone, CellGAN is equipped with a non-linear class mapping network to effectively incorporate cell type information into image generation. We also propose the Skip-layer Global Context module to model the complex spatial relationship of the cells, and attain high fidelity of the synthesized images through adversarial learning. Our experiments demonstrate that CellGAN can produce visually plausible TCT cytopathological images for different cell types. We also validate the effectiveness of using CellGAN to greatly augment patch-level cell classification performance.","PeriodicalId":18289,"journal":{"name":"Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention","volume":"86 1","pages":"487-496"},"PeriodicalIF":0.0,"publicationDate":"2023-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76346384","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}
Noisy label problems are inevitably in existence within medical image segmentation causing severe performance degradation. Previous segmentation methods for noisy label problems only utilize a single image while the potential of leveraging the correlation between images has been overlooked. Especially for video segmentation, adjacent frames contain rich contextual information beneficial in cognizing noisy labels. Based on two insights, we propose a Multi-Scale Temporal Feature Affinity Learning (MS-TFAL) framework to resolve noisy-labeled medical video segmentation issues. First, we argue the sequential prior of videos is an effective reference, i.e., pixel-level features from adjacent frames are close in distance for the same class and far in distance otherwise. Therefore, Temporal Feature Affinity Learning (TFAL) is devised to indicate possible noisy labels by evaluating the affinity between pixels in two adjacent frames. We also notice that the noise distribution exhibits considerable variations across video, image, and pixel levels. In this way, we introduce Multi-Scale Supervision (MSS) to supervise the network from three different perspectives by re-weighting and refining the samples. This design enables the network to concentrate on clean samples in a coarse-to-fine manner. Experiments with both synthetic and real-world label noise demonstrate that our method outperforms recent state-of-the-art robust segmentation approaches. Code is available at https://github.com/BeileiCui/MS-TFAL.
{"title":"Rectifying Noisy Labels with Sequential Prior: Multi-Scale Temporal Feature Affinity Learning for Robust Video Segmentation","authors":"Beilei Cui, Minqing Zhang, Mengya Xu, An-Chi Wang, Wu Yuan, Hongliang Ren","doi":"10.48550/arXiv.2307.05898","DOIUrl":"https://doi.org/10.48550/arXiv.2307.05898","url":null,"abstract":"Noisy label problems are inevitably in existence within medical image segmentation causing severe performance degradation. Previous segmentation methods for noisy label problems only utilize a single image while the potential of leveraging the correlation between images has been overlooked. Especially for video segmentation, adjacent frames contain rich contextual information beneficial in cognizing noisy labels. Based on two insights, we propose a Multi-Scale Temporal Feature Affinity Learning (MS-TFAL) framework to resolve noisy-labeled medical video segmentation issues. First, we argue the sequential prior of videos is an effective reference, i.e., pixel-level features from adjacent frames are close in distance for the same class and far in distance otherwise. Therefore, Temporal Feature Affinity Learning (TFAL) is devised to indicate possible noisy labels by evaluating the affinity between pixels in two adjacent frames. We also notice that the noise distribution exhibits considerable variations across video, image, and pixel levels. In this way, we introduce Multi-Scale Supervision (MSS) to supervise the network from three different perspectives by re-weighting and refining the samples. This design enables the network to concentrate on clean samples in a coarse-to-fine manner. Experiments with both synthetic and real-world label noise demonstrate that our method outperforms recent state-of-the-art robust segmentation approaches. Code is available at https://github.com/BeileiCui/MS-TFAL.","PeriodicalId":18289,"journal":{"name":"Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention","volume":"53 93 1","pages":"90-100"},"PeriodicalIF":0.0,"publicationDate":"2023-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78353294","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 : 2023-07-12DOI: 10.48550/arXiv.2307.06312
Shengbo Gao, Zijia Zhang, Jiechao Ma, Zilong Li, Shu Zhang
Semi-supervised learning has become increasingly popular in medical image segmentation due to its ability to leverage large amounts of unlabeled data to extract additional information. However, most existing semi-supervised segmentation methods only focus on extracting information from unlabeled data, disregarding the potential of labeled data to further improve the performance of the model. In this paper, we propose a novel Correlation Aware Mutual Learning (CAML) framework that leverages labeled data to guide the extraction of information from unlabeled data. Our approach is based on a mutual learning strategy that incorporates two modules: the Cross-sample Mutual Attention Module (CMA) and the Omni-Correlation Consistency Module (OCC). The CMA module establishes dense cross-sample correlations among a group of samples, enabling the transfer of label prior knowledge to unlabeled data. The OCC module constructs omni-correlations between the unlabeled and labeled datasets and regularizes dual models by constraining the omni-correlation matrix of each sub-model to be consistent. Experiments on the Atrial Segmentation Challenge dataset demonstrate that our proposed approach outperforms state-of-the-art methods, highlighting the effectiveness of our framework in medical image segmentation tasks. The codes, pre-trained weights, and data are publicly available.
{"title":"Correlation-Aware Mutual Learning for Semi-supervised Medical Image Segmentation","authors":"Shengbo Gao, Zijia Zhang, Jiechao Ma, Zilong Li, Shu Zhang","doi":"10.48550/arXiv.2307.06312","DOIUrl":"https://doi.org/10.48550/arXiv.2307.06312","url":null,"abstract":"Semi-supervised learning has become increasingly popular in medical image segmentation due to its ability to leverage large amounts of unlabeled data to extract additional information. However, most existing semi-supervised segmentation methods only focus on extracting information from unlabeled data, disregarding the potential of labeled data to further improve the performance of the model. In this paper, we propose a novel Correlation Aware Mutual Learning (CAML) framework that leverages labeled data to guide the extraction of information from unlabeled data. Our approach is based on a mutual learning strategy that incorporates two modules: the Cross-sample Mutual Attention Module (CMA) and the Omni-Correlation Consistency Module (OCC). The CMA module establishes dense cross-sample correlations among a group of samples, enabling the transfer of label prior knowledge to unlabeled data. The OCC module constructs omni-correlations between the unlabeled and labeled datasets and regularizes dual models by constraining the omni-correlation matrix of each sub-model to be consistent. Experiments on the Atrial Segmentation Challenge dataset demonstrate that our proposed approach outperforms state-of-the-art methods, highlighting the effectiveness of our framework in medical image segmentation tasks. The codes, pre-trained weights, and data are publicly available.","PeriodicalId":18289,"journal":{"name":"Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention","volume":"295 1","pages":"98-108"},"PeriodicalIF":0.0,"publicationDate":"2023-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75421168","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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