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H-SynEx: Using synthetic images and ultra-high resolution ex vivo MRI for hypothalamus subregion segmentation

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arXiv 2024年

作者： Rodrigues, Livia Bocchetta, Martina Puonti, Oula Greve, Douglas Londe, Ana Carolina França, Marcondes Appenzeller, Simone Iglesias, Juan Eugenio Rittner, Leticia Universidade Estadual de Campinas School of Electrical and Computer Engineering Brazil Massachusetts General Hospital Harvard Medical School United States Dementia Research Centre Department of Neurodegenerative Disease UCL Queen Square Institute of Neurology University College London London United Kingdom Centre for Cognitive and Clinical Neuroscience Division of Psychology Department of Life Sciences College of Health Medicine Life Sciences Brunel University London United Kingdom Universidade Estadual de Campinas School of Medical Sciences Brazil Centre for Medical Image Computing University College London United Kingdom Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology United States

The hypothalamus is a small structure located in the center of the brain and is involved in significant functions such as sleeping, temperature, and appetite control. Various neurological disorders are also associated with hypothalamic abnormalities. Automated image analysis of this structure from brain MRI is thus highly desirable to study the hypothalamus in vivo. However, most automated segmentation tools currently available focus exclusively on T1w images. In this study, we introduce H-SynEx, a machine learning method for automated segmentation of hypothalamic subregions that generalizes across different MRI sequences and resolutions without retraining. H-synEx was trained with synthetic images built from label maps derived from ultra-high resolution ex vivo MRI scans, which enables finer-grained manual segmentation when compared with 1mm isometric in vivo images. We validated our method using Dice Coefficient (DSC) and Average Hausdorff distance (AVD) across in vivo images from six different datasets with six different MRI sequences (T1, T2, proton density, quantitative T1, fractional anisotrophy, and FLAIR). Statistical analysis compared hypothalamic subregion volumes in controls, Alzheimer’s disease (AD), and behavioral variant frontotemporal dementia (bvFTD) subjects using the Area Under the Receiving Operating Characteristic curve (AUROC) and Wilcoxon rank sum test. Our results show that H-SynEx successfully leverages information from ultra-high resolution scans to segment in vivo from different MRI sequences. Our automated segmentation was able to discriminate controls versus Alzheimer’s Disease patients on FLAIR images with 5mm spacing. H-SynEx is openly available at https://***/liviamarodrigues/hsynex. © 2024, CC BY.

关键词： image segmentation

High-resolution segmentations of the hypothalamus and its subregions for training of segmentation models

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arXiv 2024年

作者： Rodrigues, Livia Bocchetta, Martina Puonti, Oula Greve, Douglas Londe, Ana Carolina França, Marcondes Appenzeller, Simone Rittner, Leticia Iglesias, Juan Eugenio Massachusetts General Hospital Harvard Medical School United States Universidade Estadual de Campinas School of Electrical and Computer Engineering Brazil Dementia Research Centre Department of Neurodegenerative Disease UCL Queen Square Institute of Neurology University College London London United Kingdom Centre for Cognitive and Clinical Neuroscience Division of Psychology Department of Life Sciences College of Health Medicine and Life Sciences Brunel University London United Kingdom Universidade Estadual de Campinas School of Medical Sciences Brazil Centre for Medical Image Computing University College London United Kingdom Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology United States

Segmentation of brain structures on magnetic resonance imaging (MRI) is a highly relevant neuroimaging topic, as it is a prerequisite for different analyses such as volumetry or shape analysis. Automated segmentation facilitates the study of brain structures in larger cohorts when compared with manual segmentation, which is time-consuming. However, the development of most automated methods relies on large and manually annotated datasets, which limits the generalizability of these methods. Recently, new techniques using synthetic images have emerged, reducing the need for manual annotation. Here we provide HELM, Hypothalamic ex vivo Label Maps, a dataset composed of label maps built from publicly available ultra-high resolution ex vivo MRI from 10 whole hemispheres, which can be used to develop segmentation methods using synthetic data. The label maps are obtained with a combination of manual labels for the hypothalamic regions and automated segmentations for the rest of the brain, and mirrored to simulate entire brains. We also provide the pre-processed ex vivo scans, as this dataset can support future projects to include other structures after these are manually segmented. © 2024, CC BY.

关键词： Magnetic resonance imaging

Supervision and Source Domain Impact on Representation Learning: A Histopathology Case Study

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Supervision and Source Domain Impact on Representation Learn...

Annual International Conference of the IEEE engineering in Medicine and Biology Society (EMBC)

作者： Milad Sikaroudi Amir Safarpoor Benyamin Ghojogh Sobhan Shafiei Mark Crowley H.R. Tizhoosh Laboratory for Knowledge Inference in Medical Image Analysis (Kimia Lab) University of Waterloo Waterloo ON Canada Department of Electrical and Computer Engineering University of Waterloo Waterloo ON Canada

ISBN: (数字)9781728119908

ISBN: (纸本)9781728119915

As many algorithms depend on a suitable representation of data, learning unique features is considered a crucial task. Although supervised techniques using deep neural networks have boosted the performance of representation learning, the need for a large sets of labeled data limits the application of such methods. As an example, high-quality delineations of regions of interest in the field of pathology is a tedious and time-consuming task due to the large image dimensions. In this work, we explored the performance of a deep neural network and triplet loss in the area of representation learning. We investigated the notion of similarity and dissimilarity in pathology whole-slide images and compared different setups from unsupervised and semi-supervised to supervised learning in our experiments. Additionally, different approaches were tested, applying few-shot learning on two publicly available pathology image datasets. We achieved high accuracy and generalization when the learned representations were applied to two different pathology datasets.

关键词： Pathology Cancer Neural networks Data models Lung Training Support vector machines

Segmentation of infrared breast images using MultiResUnet neural networks

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arXiv 2020年

作者： Lou, Ange Guan, Shuyue Kamona, Nada Loew, Murray Medical Imaging and Image Analysis Laboratory Department of Electrical and Computer Engineering George Washington University Medical Center WashingtonDC United States Medical Imaging and Image Analysis Laboratory Department of Biomedical Engineering George Washington University Medical Center WashingtonDC United States

Breast cancer is the second leading cause of death for women in the U.S. Early detection of breast cancer is key to higher survival rates of breast cancer patients. We are investigating infrared (IR) thermography as a noninvasive adjunct to mammography for breast cancer screening. IR imaging is radiation-free, pain-free, and non-contact. Automatic segmentation of the breast area from the acquired full-size breast IR images will help limit the area for tumor search, as well as reduce the time and effort costs of manual segmentation. Autoencoder-like convolutional and deconvolutional neural networks (C-DCNN) had been applied to automatically segment the breast area in IR images in previous studies. In this study, we applied a state-of-the-art deep-learning segmentation model, MultiResUnet, which consists of an encoder part to capture features and a decoder part for precise localization. It was used to segment the breast area by using a set of breast IR images, collected in our pilot study by imaging breast cancer patients and normal volunteers with a thermal infrared camera (N2 imager). The database we used has 450 images, acquired from 14 patients and 16 volunteers. We used a thresholding method to remove interference in the raw images and remapped them from the original 16-bit to 8-bit, and then cropped and segmented the 8-bit images manually. Experiments using leave-one-out cross-validation (LOOCV) and comparison with the ground-truth images by using Tanimoto similarity show that the average accuracy of MultiResUnet is 91.47%, which is about 2% higher than that of the autoencoder. MultiResUnet offers a better approach to segment breast IR images than our previous model. Copyright © 2020, The Authors. All rights reserved.

关键词： computer aided diagnosis

DC-UNet: Rethinking the U-Net architecture with dual channel efficient CNN for medical images segmentation

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arXiv 2020年

作者： Lou, Ange Guan, Shuyue Loew, Murray Medical Imaging and Image Analysis Laboratory Department of Electrical and Computer Engineering George Washington University Medical Center WashingtonDC United States Medical Imaging and Image Analysis Laboratory Department of Biomedical Engineering George Washington University Medical Center WashingtonDC United States

Recently, deep learning has become much more popular in computer vision area. The Convolution Neural Network (CNN) has brought a breakthrough in images segmentation areas, especially, for medical images. In this regard, U-Net is the predominant approach to medical image segmentation task. The U-Net not only performs well in segmenting multimodal medical images generally, but also in some tough cases of them. However, we found that the classical U-Net architecture has limitation in several aspects. Therefore, we applied modifications: 1) designed efficient CNN architecture to replace encoder and decoder, 2) applied residual module to replace skip connection between encoder and decoder to improve based on the-state-of-the-art U-Net model. Following these modifications, we designed a novel architecture--DC-UNet, as a potential successor to the U-Net architecture. We created a new effective CNN architecture and build the DC-UNet based on this CNN. We have evaluated our model on three datasets with tough cases and have obtained a relative improvement in performance of 2.90%, 1.49% and 11.42% respectively compared with classical U-Net. In addition, we used the Tanimoto similarity to replace the Jaccard similarity for gray-to-gray image comparisons. Copyright © 2020, The Authors. All rights reserved.

关键词： image segmentation

180-degree outpainting from a single image

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arXiv 2020年

作者： Ying, Zhenqiang Bovik, Alan C. Laboratory for Image and Video Engineering Department of Electrical and Computer Engineering University of Texas at Austin AustinTX78712 United States

Presenting context images to a viewer's peripheral vision is one of the most effective techniques to enhance immersive visual experiences. However, most images only present a narrow view, since the field-of-view (FoV) of standard cameras is small. To overcome this limitation, we propose a deep learning approach that learns to predict a 180-degree panoramic image from a narrow-view image. Specifically, we design a foveated framework that applies different strategies on near-periphery and mid-periphery regions. Two networks are trained separately, and then are employed jointly to sequentially perform narrow-to-90° generation and 90°-to-180° generation. The generated outputs are then fused with their aligned inputs to produce expanded equirectangular images for viewing. Our experimental results show that single-view-to-panoramic image generation using deep learning is both feasible and promising. Copyright © 2020, The Authors. All rights reserved.

关键词： Augmented reality

A comprehensive review of computer-aided whole-slide image analysis: From datasets to feature extraction, segmentation, classification and detection approaches

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arXiv 2021年

作者： Li, Chen Li, Xintong Rahaman, Md Li, Xiaoyan Sun, Hongzan Zhang, Hong Zhang, Yong Li, Xiaoqi Wu, Jian Yao, Yudong Grzegorzek, Marcin Microscopic Image and Medical Image Analysis Group College of Medicine and Biological Information Engineering Northeastern University Shenyang110169 China China Medical University Shenyang110122 China Department of Electrical and Computer Engineering Stevens Institute of Technology Hobo-kenNJ07030 United States Institute of Medical Informatics University of Luebeck Luebeck Germany

With the development of computer-aided diagnosis (CAD) and image scanning technology, Whole-slide image (WSI) scanners are widely used in the field of pathological diagnosis. Therefore, WSI analysis has become the key to modern digital pathology. Since 2004, WSI has been used more and more in CAD. Since machine vision methods are usually based on semi-automatic or fully automatic computers, they are highly efficient and labor-saving. The combination of WSI and CAD technologies for segmentation, classification, and detection helps histopathologists obtain more stable and quantitative analysis results, save labor costs and improve diagnosis objectivity. This paper reviews the methods of WSI analysis based on machine learning. Firstly, the development status of WSI and CAD methods are introduced. Secondly, we discuss publicly available WSI datasets and evaluation metrics for segmentation, classification, and detection tasks. Then, the latest development of machine learning in WSI segmentation, classification, and detection are reviewed continuously. Finally, the existing methods are studied, the applicability of the analysis methods are analyzed, and the application prospects of the analysis methods in this field are forecasted. © 2021, CC BY.

关键词： image segmentation

MyoPS: A Benchmark of Myocardial Pathology Segmentation Combining Three-Sequence Cardiac Magnetic Resonance images

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arXiv 2022年

作者： Li, Lei Wu, Fuping Wang, Sihan Luo, Xinzhe Martín-Isla, Carlos Zhai, Shuwei Zhang, Jianpeng Liu, Yanfei Zhang, Zhen Ankenbrand, Markus J. Jiang, Haochuan Zhang, Xiaoran Wang, Linhong Arega, Tewodros Weldebirhan Altunok, Elif Zhao, Zhou Li, Feiyan Ma, Jun Yang, Xiaoping Puybareau, Elodie Oksuz, Ilkay Bricq, Stephanie Li, Weisheng Punithakumar, Kumaradevan Tsaftaris, Sotirios A. Schreiber, Laura M. Yang, Mingjing Liu, Guocai Xia, Yong Wang, Guotai Escalera, Sergio Zhuang, Xiahai School of Data Science Fudan University Shanghai China School of Biomedical Engineering Shanghai Jiao Tong University Shanghai China Departament de Matemàtiques & Informàtica Universitat de Barcelona Barcelona Spain Computer Vision Center Universitat Autònoma de Barcelona Spain School of Mechanical and Electrical Engineering University of Electronic Science and Technology of China Chengdu China School of Computer Science and Engineering Northwestern Polytechnical University Xi'An China College of Electrical and Information Engineering Hunan University Changsha China National Engineering Laboratory for Robot Visual Perception and Control Technology Changsha China College of Physics and Information Engineering Fuzhou University Fuzhou China Comprehensive Heart Failure Center Wuerzburg University Hospitals Wuerzburg Germany School of Engineering University of Edinburgh Edinburgh United Kingdom School of Robotics Xi'an Jiaotong-Liverpool University Suzhou China Department of Electrical and Computer Engineering University of California Los Angeles United States Department of Radiology and Diagnostic Imaging University of Alberta Edmonton Canada Chongqing Key Laboratory of Image Cognition Chongqing University of Posts and Telecomm-Unications Chongqing China ImViA Laboratory Université Bourgogne Franche-Comté Dijon France Computer Engineering Department Istanbul Technical University Istanbul Turkey Le Kremlin-Bicêtre France Department of Mathematics Nanjing University of Science and Technology Nanjing China Department of Mathematics Nanjing University Nanjing China

Assessment of myocardial viability is essential in diagnosis and treatment management of patients suffering from myocardial infarction, and classification of pathology on myocardium is the key to this assessment. This work defines a new task of medical image analysis, i.e., to perform myocardial pathology segmentation (MyoPS) combining three-sequence cardiac magnetic resonance (CMR) images, which was first proposed in the MyoPS challenge, in conjunction with MICCAI 2020. The challenge provided 45 paired and pre-aligned CMR images, allowing algorithms to combine the complementary information from the three CMR sequences for pathology segmentation. In this article, we provide details of the challenge, survey the works from fifteen participants and interpret their methods according to five aspects, i.e., preprocessing, data augmentation, learning strategy, model architecture and post-processing. In addition, we analyze the results with respect to different factors, in order to examine the key obstacles and explore potential of solutions, as well as to provide a benchmark for future research. We conclude that while promising results have been reported, the research is still in the early stage, and more in-depth exploration is needed before a successful application to the clinics. Note that MyoPS data and evaluation tool continue to be publicly available upon registration via its homepage (***/zhuangxiahai/0/myops20/). © 2022, CC BY-NC-SA.

关键词： Magnetic resonance imaging

Towards Phytoplankton Parasite Detection Using Autoencoders

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arXiv 2023年

作者： Bilik, Simon Batrakhanov, Daniel Eerola, Tuomas Haraguchi, Lumi Kraft, Kaisa Van den Wyngaert, Silke Kangas, Jonna Sjöqvist, Conny Madsen, Karin Lensu, Lasse Kälviäinen, Heikki Horak, Karel Computer Vision and Pattern Recognition Laboratory Department of Computational Engineering Lappeenranta-Lahti University of Technology LUT Yliopistonkatu 34 Lappeenranta53850 Finland Department of Control and Instrumentation Faculty of Electrical Engineering and Communication Brno University of Technology Technická 3058/10 Brno61600 Czech Republic Marine Ecology Measurements Finnish Environment Institute Agnes Sjöbergin Katu 2 Helsinki00790 Finland Department of Biology University of Turku Vesilinnantie 5 Turku20014 Finland Environmental and Marine Biology Åbo Akademi University Henrikinkatu 2 Turku20014 Finland

Phytoplankton parasites are largely understudied microbial components with a potentially significant ecological impact on phytoplankton bloom dynamics. To better understand their impact, we need improved detection methods to integrate phytoplankton parasite interactions in monitoring aquatic ecosystems. Automated imaging devices usually produce high amount of phytoplankton image data, while the occurrence of anomalous phytoplankton data is rare. Thus, we propose an unsupervised anomaly detection system based on the similarity of the original and autoencoder-reconstructed samples. With this approach, we were able to reach an overall F1 score of 0.75 in nine phytoplankton species, which could be further improved by species-specific fine-tuning. The proposed unsupervised approach was further compared with the supervised Faster R-CNN based object detector. With this supervised approach and the model trained on plankton species and anomalies, we were able to reach the highest F1 score of 0.86. However, the unsupervised approach is expected to be more universal as it can detect also unknown anomalies and it does not require any annotated anomalous data that may not be always available in sufficient quantities. Although other studies have dealt with plankton anomaly detection in terms of non-plankton particles, or air bubble detection, our paper is according to our best knowledge the first one which focuses on automated anomaly detection considering putative phytoplankton parasites or infections. © 2023, CC BY.

关键词： Object detection