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A State-of-the-art Survey of Object Detection Techniques in Microorganism image analysis: From Classical Methods to Deep Learning Approaches

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arXiv 2021年

作者： Ma, Pingli Li, Chen Rahaman, Md Mamunur Yao, Yudong Zhang, Jiawei Zou, Shuojia Zhao, Xin Grzegorzek, Marcin Microscopic Image and Medical Image Analysis Group Medicine and Biological Information Engineering College Northeastern University China Department of Electrical and Computer Engineering Stevens Institute of Technology United States Biomedical Information College University of Luebeck Germany

Microorganisms play a vital role in human life. Therefore, microorganism detection is of great significance to human beings. However, the traditional manual microscopic detection methods have the disadvantages of long detection cycle, low detection accuracy in large orders, and great difficulty in detecting uncommon microorganisms. Therefore, it is meaningful to apply computer image analysis technology to the field of microorganism detection. computer image analysis can realize high-precision and high-efficiency detection of microorganisms. In this review, first,we analyse the existing microorganism detection methods in chronological order, from traditional image processing and traditional machine learning to deep learning methods. Then, we analyze and summarize these existing methods and introduce some potential methods, including visual transformers. In the end, the future development direction and challenges of microorganism detection are discussed. In general, we have summarized 142 related technical papers from 1985 to the present. This review will help researchers have a more comprehensive understanding of the development process, research status, and future trends in the field of microorganism detection and provide a reference for researchers in other fields. © 2021, CC BY.

关键词： Microorganisms

Semi-Supervised and Self-Supervised Collaborative Learning for Prostate 3D MR image Segmentation

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Semi-Supervised and Self-Supervised Collaborative Learning f...

IEEE International Symposium on Biomedical Imaging

作者： Yousuf Babiker M. Osman Cheng Li Weijian Huang Nazik Elsayed Leslie Ying Hairong Zheng Shanshan Wang Paul C. Lauterbur Research Center for Biomedical Imaging Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen China University of Chinese Academy of Sciences Beijing China Faculty of Mathematical and Computer Sciences University of Gezira Wad Madani Sudan Department of Biomedical Engineering and Department of Electrical Engineering University at Buffalo The State University of New York New York USA Guangdong Provincial Key Laboratory of Artificial Intelligence in Medical Image Analysis and Application Guangdong China

Volumetric magnetic resonance (MR) image segmentation plays an important role in many clinical applications. Deep learning (DL) has recently achieved state-of-the-art or even human-level performance on various image segmentation tasks. Nevertheless, manually annotating volumetric MR images for DL model training is labor-exhaustive and time-consuming. In this work, we aim to train a semi-supervised and self-supervised collaborative learning framework for prostate 3D MR image segmentation while using extremely sparse annotations, for which the ground truth annotations are provided for just the central slice of each volumetric MR image. Specifically, semi-supervised learning and self-supervised learning methods are used to generate two independent sets of pseudo labels. These pseudo labels are then fused by the Boolean operation to extract a more confident pseudo label set. The images with either manual or network self-generated labels are then employed to train a segmentation model for target volume extraction. Experimental results on a publicly available prostate MR image dataset demonstrate that, while requiring significantly less annotation effort, our framework generates very encouraging segmentation results. The proposed framework is very useful in clinical applications when training data with dense annotations are difficult to obtain.

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A Comprehensive Survey with Quantitative Comparison of image analysis Methods for Microorganism Biovolume Measurements

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arXiv 2022年

作者： Zhang, Jiawei Li, Chen Rahaman, Md Mamunur Yao, Yudong Ma, Pingli Zhang, Jinghua Zhao, Xin Jiang, Tao Grzegorzek, Marcin Microscopic Image and Medical Image Analysis Group College of Medicine and Biological Information Engineering Northeastern University Shenyang110169 China Department of Electrical and Computer Engineering Stevens Institute of Technology HobokenNJ07030 United States School of Resources and Civil Engineering Northeastern University Shenyang110004 China School of Control Engineering Chengdu University of Information Technology Chengdu610225 China Institute of Medical Informatics University of Luebeck Luebeck23538 Germany School of Computer Science and Engineering University of New South Wales SydneyNSW2052 Australia

With the acceleration of urbanization and living standards, microorganisms play an increasingly important role in industrial production, bio-technique, and food safety testing. Microorganism biovolume measurements are one of the essential parts of microbial analysis. However, traditional manual measurement methods are time-consuming and challenging to measure the characteristics precisely. With the development of digital image processing techniques, the characteristics of the microbial population can be detected and quantified. The applications of the microorganism biovolume measurement method have developed since the 1980s. More than 62 articles are reviewed in this study, and the articles are grouped by digital image analysis methods with time. This study has high research significance and application value, which can be referred to as microbial researchers to comprehensively understand microorganism biovolume measurements using digital image analysis methods and potential applications. © 2022, CC0.

关键词： Microorganisms

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

Touchstone benchmark: are we on the right way for evaluating AI algorithms for medical segmentation? 24

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Touchstone benchmark: are we on the right way for evaluating...

Proceedings of the 38th International Conference on Neural Information Processing Systems

作者： Pedro R. A. S. Bassi Wenxuan Li Yucheng Tang Fabian Isensee Zifu Wang Jieneng Chen Yu-Cheng Chou Saikat Roy Yannick Kirchhoff Maximilian Rokuss Ziyan Huang Jin Ye Junjun He Tassilo Wald Constantin Ulrich Michael Baumgartner Klaus H. Maier-Hein Paul Jaeger Yiwen Ye Yutong Xie Jianpeng Zhang Ziyang Chen Yong Xia Zhaohu Xing Lei Zhu Yousef Sadegheih Afshin Bozorgpour Pratibha Kumari Reza Azad Dorit Merhof Pengcheng Shi Ting Ma Yuxin Du Fan Bai Tiejun Huang Bo Zhao Haonan Wang Xiaomeng Li Hanxue Gu Haoyu Dong Jichen Yang Maciej A. Mazurowski Saumya Gupta Linshan Wu Jiaxin Zhuang Hao Chen Holger Roth Daguang Xu Matthew B. Blaschko Sergio Decherchi Andrea Cavalli Alan L. Yuille Zongwei Zhou Department of Computer Science Johns Hopkins University and Department of Pharmacy and Biotechnology University of Bologna and Center for Biomolecular Nanotechnologies Istituto Italiano di Tecnologia Department of Computer Science Johns Hopkins University NVIDIA Division of Medical Image Computing German Cancer Research Center (DKFZ) and Helmholtz Imaging German Cancer Research Center (DKFZ) ESAT-PSI KU Leuven Division of Medical Image Computing German Cancer Research Center (DKFZ) and Faculty of Mathematics and Computer Science Heidelberg University Division of Medical Image Computing German Cancer Research Center (DKFZ) and Faculty of Mathematics and Computer Science Heidelberg University and HIDSS4Health - Helmholtz Information and Data Science School for Health Shanghai Jiao Tong University Shanghai Artificial Intelligence Laboratory Division of Medical Image Computing German Cancer Research Center (DKFZ) Division of Medical Image Computing German Cancer Research Center (DKFZ) and Pattern Analysis and Learning Group Department of Radiation Oncology Heidelberg University Hospital Helmholtz Imaging German Cancer Research Center (DKFZ) and Interactive Machine Learning Group (IML) DKFZ School of Computer Science and Engineering Northwestern Polytechnical University Australian Institute for Machine Learning The University of Adelaide College of Computer Science and Technology Zhejiang University Hong Kong University of Science and Technology (Guangzhou) Hong Kong University of Science and Technology (Guangzhou) and Hong Kong University of Science and Technology Faculty of Informatics and Data Science University of Regensburg Faculty of Electrical Engineering and Information Technology RWTH Aachen University Faculty of Informatics and Data Science University of Regensburg and Fraunhofer Institute for Digital Medicine MEVIS Electronic & Information Engineering School Harbin Institute of Technology (Shenzhen) Shanghai Jiao Tong University and Beijing Academy of Artificial Intelligence (BAAI) S

ISBN: (纸本)9798331314385

How can we test AI performance? This question seems trivial, but it isn't. Standard benchmarks often have problems such as in-distribution and small-size test sets, oversimplified metrics, unfair comparisons, and short-term outcome pressure. As a consequence, good performance on standard benchmarks does not guarantee success in real-world scenarios. To address these problems, we present Touchstone, a large-scale collaborative segmentation benchmark of 9 types of abdominal organs. This benchmark is based on 5,195 training CT scans from 76 hospitals around the world and 5,903 testing CT scans from 11 additional hospitals. This diverse test set enhances the statistical significance of benchmark results and rigorously evaluates AI algorithms across out-of-distribution scenarios. We invited 14 inventors of 19 AI algorithms to train their algorithms, while our team, as a third party, independently evaluated these algorithms. In addition, we also evaluated pre-existing AI frameworks—which, differing from algorithms, are more flexible and can support different algorithms—including MONAI from NVIDIA, nnU-Net from DKFZ, and numerous other open-source frameworks. We are committed to expanding this benchmark to encourage more innovation of AI algorithms for the medical domain.

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Enhancing Medical image Segmentation with TransCeption: A Multi-Scale Feature Fusion Approach

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arXiv 2023年

作者： Azad, Reza Jia, Yiwei Aghdam, Ehsan Khodapanah Cohen-Adad, Julien Merhof, Dorit The Institute of Imaging and Computer Vision RWTH Aachen University Aachen52074 Germany The Department of Electrical Engineering Shahid Beheshti University Tehran*** Iran The Mila Quebec AI Institute Canada The Functional Neuroimaging Unit CRIUGM University of Montreal Canada The NeuroPoly Lab Institute of Biomedical Engineering Polytechnique Montreal MontrealH3T 1J4 Canada The Institute of Image Analysis and Computer Vision Faculty of Informatics and Data Science University of Regensburg Regensburg93053 Germany The Fraunhofer Institute for Digital Medicine MEVIS Bremen28359 Germany

While CNN-based methods have been the cornerstone of medical image segmentation due to their promising performance and robustness, they suffer from limitations in capturing long-range dependencies. Transformer-based approaches are currently prevailing since they enlarge the reception field to model global contextual correlation. To further extract rich representations, some extensions of the U-Net employ multi-scale feature extraction and fusion modules and obtain improved performance. Inspired by this idea, we propose TransCeption for medical image segmentation, a pure transformer-based U-shape network featured by incorporating the inception-like module into the encoder and adopting a contextual bridge for better feature fusion. The design proposed in this work is based on three core principles: (1) The patch merging module in the encoder is redesigned with ResInception Patch Merging (RIPM). Multi-branch transformer (MB transformer) adopts the same number of branches as the outputs of RIPM. Combining the two modules enables the model to capture a multi-scale representation within a single stage. (2) We construct an Intra-stage Feature Fusion (IFF) module following the MB transformer to enhance the aggregation of feature maps from all the branches and particularly focus on the interaction between the different channels of all the scales. (3) In contrast to a bridge that only contains token-wise self-attention, we propose a Dual Transformer Bridge that also includes channel-wise self-attention to exploit correlations between scales at different stages from a dual perspective. Extensive experiments on multi-organ and skin lesion segmentation tasks present the superior performance of TransCeption compared to previous work. The code is publicly available on GitHub. © 2023, CC BY.

关键词： Merging

Discrete, recurrent, and scalable patterns in human judgement underlie affective picture ratings

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arXiv 2022年

作者： Azcona, Emanuel A. Kim, Byoung-Woo Vike, Nicole L. Bari, Sumra Lalvani, Shamal Stefanopoulos, Leandros Woodward, Sean Block, Martin Katsaggelos, Aggelos K. Breiter, Hans C. Image and Video Processing Lab Department of Electrical and Computer Engineering Northwestern University EvanstonIL United States Department of Psychiatry and Behavioral Sciences Northwestern University ChicagoIL United States Integrated Marketing Communications Northwestern University EvanstonIL United States Department of Computer Science Northwestern University EvanstonIL United States Department of Radiology Northwestern University ChicagoIL United States Laboratory of Neuroimaging and Genetics Department of Psychiatry Massachusetts General Hospital Harvard School of Medicine BostonMA United States

Operant keypress tasks, where each action has a consequence, have been analogized to the construct of "wanting" and produce lawful relationships in humans that quantify preferences for approach and avoidance behavior. It is unknown if rating tasks without an operant framework, which can be analogized to "liking", show similar lawful relationships. We studied three independent cohorts of participants (N = 501, 506, and 4,019 participants) collected by two distinct organizations, using the same 7-point Likert scale to rate negative to positive preferences for pictures from the International Affective Picture Set. Picture ratings without an operant framework produced similar value functions, limit functions, and tradeoff functions to those reported in the literature for operant keypress tasks, all with Rn goodness of fits above 0.75. These value, limit, and trade-off functions were discrete in their mathematical formulation, recurrent across all three independent cohorts, and demonstrated scaling between individual and group curves. In all three experiments, the computation of loss aversion showed 95% confidence intervals below the value of 2, arguing against a strong overweighting of losses relative to gains, as has previously been reported for keypress tasks or games of chance with calibrated uncertainty. Graphed features from the three cohorts were similar and argue that preference assessments meet three of four criteria for lawfulness, providing a simple, short, and low-cost method for the quantitative assessment of preference without forced choice decisions, games of chance, or operant keypressing. This approach can easily be implemented on any digital device with a screen (e.g., cellphones). © 2022, CC BY.

关键词： Big data

EBHI: A new enteroscope biopsy histopathological H&E image dataset for image classification evaluation

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arXiv 2022年

作者： Hu, Weiming Li, Chen Li, Xiaoyan Rahaman, Md Mamunur Zhang, Yong Chen, Haoyuan Liu, Wanli Yao, Yudong Sun, Hongzan Xu, Ning Huang, Xinyu Grzegorzek, Marcin Microscopic Image And Medical Image Analysis Group MBIE College Northeastern University Shenyang110169 China Department Of Pathology Cancer Hospital China Medical University Liaoning Cancer Hospital And Institute Shenyang110042 China School Of Computer Science And Engineering University Of New South Wales SydneyNSW2052 Australia Department Of Electrical And Computer Engineering Stevens Institute Of Technology HobokenNJ07030 United States Department Of Radiology Shengjing Hospital China Medical University Shenyang110122 China School Of Arts And Design Liaoning Shihua University Fushun113001 China Institute Of Medical Informatics University Of Luebeck Luebeck Germany

Background and purpose: Colorectal cancer has become the third most common cancer worldwide, accounting for approximately 10% of cancer patients. Early detection of the disease is important for the treatment of colorectal cancer patients. Histopathological examination is the gold standard for screening colorectal cancer. However, the current lack of histopathological image datasets of colorectal cancer, especially enteroscope biopsies, hinders the accurate evaluation of computer-aided diagnosis techniques. Methods: A new publicly available Enteroscope Biopsy Histopathological H&E image Dataset (EBHI) is published in this paper. To demonstrate the effectiveness of the EBHI dataset, we have utilized several machine learning, convolutional neural networks and novel transformer-based classifiers for experimentation and evaluation, using an image with a magnification of 200×. Results: Experimental results show that the deep learning method performs well on the EBHI dataset. Traditional machine learning methods achieve maximum accuracy of 76.02% and deep learning method achieves a maximum accuracy of 95.37%. Conclusion: To the best of our knowledge, EBHI is the first publicly available colorectal histopathology enteroscope biopsy dataset with four magnifications and five types of images of tumor differentiation stages, totaling 5532 images. We believe that EBHI could attract researchers to explore new classification algorithms for the automated diagnosis of colorectal cancer, which could help physicians and patients in clinical settings. Copyright © 2022, The Authors. All rights reserved.

关键词： image classification

DF-DM: A foundational process model for multimodal data fusion in the artificial intelligence era

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arXiv 2024年

作者： Restrepo, David Wu, Chenwei Vásquez-Venegas, Constanza Nakayama, Luis Filipe Celi, Leo Anthony López, Diego M. Laboratory for Computational Physiology Massachusetts Institute of Technology CambridgeMA United States Departamento de Telemática Universidad del Cauca Cauca Popayán Colombia Department of Electrical Engineering and Computer Science University of Michigan Ann ArborMI United States Scientific Image Analysis Lab Universidad de Chile Santiago Santiago Chile Department of Ophthalmology São Paulo Federal University São Paulo São Paulo Brazil Department of Biostatistics Harvard TH Chan School of Public Health BostonMA United States Department of Medicine Beth Israel Deaconess Medical Center BostonMA United States

In the big data era, integrating diverse data modalities poses significant challenges, particularly in complex fields like healthcare. This paper introduces a new process model for multimodal Data Fusion for Data Mining, integrating embeddings and the Cross-Industry Standard Process for Data Mining with the existing Data Fusion Information Group model. Our model aims to decrease computational costs, complexity, and bias while improving efficiency and reliability. We also propose"disentangled dense fusion," a novel embedding fusion method designed to optimize mutual information and facilitate dense inter-modality feature interaction, thereby minimizing redundant information. We demonstrate the model’s efficacy through three use cases: predicting diabetic retinopathy using retinal images and patient metadata, domestic violence prediction employing satellite imagery, internet, and census data, and identifying clinical and demographic features from radiography images and clinical notes. The model achieved a Macro F1 score of 0.92 in diabetic retinopathy prediction, an R-squared of 0.854 and sMAPE of 24.868 in domestic violence prediction, and a macro AUC of 0.92 and 0.99 for disease prediction and sex classification, respectively, in radiological analysis. These results underscore the Data Fusion for Data Mining model’s potential to significantly impact multimodal data processing, promoting its adoption in diverse, resource-constrained *** Codes 68T30 © 2024, CC BY.

关键词： Forecasting