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Swin transformer-based shape-from-focus technique for accurate 3D shape estimation

Optics and Lasers in Engineering 2025年 193卷

作者： Dogan, Ramazan Ozgur Dogan, Hulya Yilmaz, Alper Department of Artificial Intelligence Engineering Faculty of Computer and Information Sciences Trabzon University Trabzon Turkey Department of Software Engineering Faculty of Engineering Karadeniz Technical University Trabzon Turkey Drug and Pharmaceutical Technology Application & Research Center Karadeniz Technical University Trabzon Turkey Photogrammetric Computer Vision Laboratory The Ohio State University Columbus United States

Accurately estimating the three-dimensional (3D) shape of an object from two-dimensional (2D) images is a fundamental challenge in computer vision, with widespread applications in fields such as biomedical imaging and microscopy. Shape-from-Focus (SFF) is a widely adopted technique for addressing this challenge, relying on focus measures from image series captured at varying focal lengths. However, existing SFF techniques often face limitations such as inadequate performance in low-texture regions, sensitivity to noise, and high computational costs when processing high-resolution image series, hindering their effectiveness in real-world applications. To address these limitations, this study proposes a novel SFF technique based on the Swin Transformer, which introduces a hierarchical feature extraction framework and integrates a spatial frequency-based focus function directly into the deep feature space. This enables more robust focus-level detection and improved accuracy in 3D shape estimation for both real and simulated image series. The main contributions include multi-scale attention-based feature modeling and an enhanced sharpness evaluation strategy, yielding superior performance across various data sets. To validate the effectiveness of the proposed technique, extensive experiments are conducted using standard evaluation metrics, complemented by qualitative comparisons via reconstructed 3D shapes. The results consistently demonstrate that the Swin Transformer-based model outperforms existing SFF techniques in both quantitative and visual analyses. These findings highlight the robustness and innovation of the proposed SFF technique, establishing it as a reliable and efficient solution for 3D shape estimation. © 2025 Elsevier Ltd

关键词： Photointerpretation

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Dilemma in All-optical Characterization of Single-layer NiI2 Multiferroics

arXiv

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arXiv 2023年

作者： Jiang, Yucheng Wu, Yangliu Zhang, Jinlei Wei, Jingxuan Peng, Bo Qiu, Cheng-Wei Department of Electrical and Computer Engineering National University of Singapore 4 Engineering Drive 3 Singapore117583 Singapore Jiangsu Key Laboratory of Micro and Nano Heat Fluid Flow Technology and Energy Application School of Physical Science and Technology Suzhou University of Science and Technology Suzhou215009 China 8 Somapah Road Singapore487372 Singapore National Engineering Research Center of Electromagnetic Radiation Control Materials School of Electronic Science and Engineering University of Electronic Science and Technology of China Chengdu611731 China

The search for two-dimensional multiferroic materials is an exciting yet challenging endeavor. Recently, Song et al. reported the exciting discovery of type-II multiferroic order in an antiferromagnetic (AFM) NiI2 single layer, and concluded the ferroelectric (FE) polarization induced by a helical magnetic order1. Their finding was presented from all-optical experimental evidence, based on the methods of second harmonic generation (SHG) and linear dichroism (LD). However, the all-optical characterizations alone cannot serve as unanimous evidence of the "FE" existence, particularly in conjunction with magnetic orders in a single-layer multiferroic. A main argument is that their observed SHG and LD signals may just be manifested from the magnetic-order induced breaking of spatial-inversion or time-reversal symmetry instead of FE order, and thus cannot endorse the finding of a single-layer multiferroic. Accurate measurements of magnetic and electric orders are very essential to make a reliable judgement of a multiferroic. With the device’s thickness approaching atomic scale, its magnetic or electrical signals will become too weak to be collected by traditional measurements2. Therefore, advanced all-optical probing methods have been © 2023, CC BY-NC-SA.

关键词： Harmonic generation

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An artificially intelligent magnetic resonance spectroscopy quantification method: Comparison between QNet and LCModel on the cloud computing platform CloudBrain-MRS

arXiv

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arXiv 2025年

作者： Lin, Meijin Guo, Lin Chen, Dicheng Chen, Jianshu Tu, Zhangren Huang, Xu Wang, Jianhua Qi, Ji Long, Yuan Huang, Zhiguo Guo, Di Qu, Xiaobo Han, Haiwei College of Ocean & Earth Sciences Xiamen University Xiamen361102 China Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance Xiamen University Xiamen361102 China National Integrated Circuit Industry Education Integration Innovation Platform Xiamen University Xiamen361100 China Department of Electronic Science Xiamen University Xiamen361102 China Department of Radiology the First Affiliated Hospital of Xiamen University School of Medicine Xiamen University Xiamen361100 China Software Technology Company Limited Suzhou215163 China School of Computer and Information Engineering Fujian Engineering Research Center for Medical Data Mining and Application Xiamen University of Technology Xiamen361024 China

Objctives: This work aimed to statistically compare the metabolite quantification of human brain magnetic resonance spectroscopy (MRS) between the deep learning method QNet and the classical method LCModel through an easy-to-use intelligent cloud computing platform CloudBrain-MRS. Materials and Methods: In this retrospective study, two 3 T MRI scanners Philips Ingenia and Achieva collected 61 and 46 in vivo 1H magnetic resonance (MR) spectra of healthy participants, respectively, from the brain region of pregenual anterior cingulate cortex from September to October 2021. The analyses of Bland-Altman, Pearson correlation and reasonability were performed to assess the degree of agreement, linear correlation and reasonability between the two quantification methods. Results: Fifteen healthy volunteers (12 females and 3 males, age range: 21-35 years, mean age ± standard deviation = 27.4 ± 3.9 years) were recruited. The analyses of Bland-Altman, Pearson correlation and reasonability showed high to good consistency and very strong to moderate correlation between the two methods for quantification of total N-acetylaspartate (tNAA), total choline (tCho), and inositol (Ins) (relative half interval of limits of agreement = 3.04%, 9.3%, and 18.5%, respectively;Pearson correlation coefficient r = 0.775, 0.927, and 0.469, respectively). In addition, quantification results of QNet are more likely to be closer to the previous reported average values than those of LCModel. Conclusion: There were high or good degrees of consistency between the quantification results of QNet and LCModel for tNAA, tCho, and Ins, and QNet generally has more reasonable quantification than LCModel. © 2025, CC BY.

关键词： Metabolites

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Segmentation of Non-Small Cell Lung Carcinomas: Introducing DRU-Net and Multi-Lens Distortion

arXiv

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arXiv 2024年

作者： Oskouei, Soroush Valla, Marit Pedersen, André Smistad, Erik Dale, Vibeke Grotnes Høibø, Maren Wahl, Sissel Gyrid Freim Haugum, Mats Dehli Langø, Thomas Ramnefjell, Maria Paula Akslen, Lars Andreas Kiss, Gabriel Sorger, Hanne Department of Circulation and Medical Imaging TrondheimNO-7491 Norway Levanger hospital Nord-Trøndelag Health Trust Clinic of Medicine LevangerNO-7600 Norway Department of Clinical and Molecular Medicine TrondheimNO-7491 Norway St. Olavs hospital Trondheim University Hospital Clinic of Laboratory Medicine TrondheimNO-7030 Norway St. Olavs hospital Trondheim University Hospital Department of Pathology TrondheimNO-7030 Norway St. Olavs hospital Trondheim University Hospital Clinic of Surgery TrondheimNO-7030 Norway Sopra Steria Application Solutions TrondheimNO-7010 Norway SINTEF Digital Department of Health Research TrondheimNO-7465 Norway St. Olavs hospital Trondheim University Hospital Research Department Center for Medical equipment Technology and Innovation TrondheimNO-7491 Norway BergenNO-5007 Norway Haukeland University Hospital Department of Pathology BergenNO-5020 Norway Department of Computer Science TrondheimNO-7491 Norway

Considering the increased workload in pathology laboratories today, automated tools such as artificial intelligence models can help pathologists with their tasks and ease the workload. In this paper, we are proposing a segmentation model (DRU-Net) that can provide a delineation of human non-small cell lung carcinomas and an augmentation method that can improve classification results. The proposed model is a fused combination of truncated pre-trained DenseNet201 and ResNet101V2 as a patch-wise classifier followed by a lightweight U-Net as a refinement model. We have used two datasets (Norwegian Lung Cancer Biobank and Haukeland University Hospital lung cancer cohort) to create our proposed model. The DRU-Net model achieves an average of 0.91 Dice similarity coefficient. The proposed spatial augmentation method (multi-lens distortion) improved the network performance by 3%. Our findings show that choosing image patches that specifically include regions of interest leads to better results for the patch-wise classifier compared to other sampling methods. The qualitative analysis showed that the DRU-Net model is generally successful in detecting the tumor. On the test set, some of the cases showed areas of false positive and false negative segmentation in the periphery, particularly in tumors with inflammatory and reactive *** Codes I.4.6 © 2024, CC BY.

关键词： Tumors

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Current Progress and Challenges in Large-scale 3D Mitochondria Instance Segmentation

TechRxiv

引用

TechRxiv 2023年

作者： Franco-Barranco, Daniel Lin, Zudi Jang, Won-Dong Wang, Xueying Shen, Qijia Yin, Wenjie Fan, Yutian Li, Mingxing Chen, Chang Xiong, Zhiwei Xin, Rui Liu, Hao Chen, Huai Li, Zhili Zhao, Jie Chen, Xuejin Pape, Constantin Conrad, Ryan De Folter, Jozefus Nightingale, Luke Jones, Martin L. Liu, Yanling Ziaei, Dorsa Huschauer, Stephan Arganda-Carreras, Ignacio Pfister, Hanspeter Wei, Donglai The Department of Computer Science and Artificial Intelligence University of the Basque Country Donostia-San Sebastian Spain San Sebastian Spain Ikerbasque Basque Foundation for Science Bilbao Spain Biofisika Institute CSIC UPV/EHU Bilbao Spain Harvard University All-ston MA United States The Department of Molecular and Cellular Biology Harvard University CambridgeMA United States The Wellcome Centre for Integrative Neuroimaging FMRIB Nuffield Department of Clinical Neurosciences University of Oxford Oxford United Kingdom University of Science and Technology of China Anhui China The Institute of Image Processing and Pattern Recognition Department of Automation Shanghai Jiao Tong University Shanghai China The National Engineering Laboratory for Brain-inspired Intelligence Technology and Application University of Science and Technology of China Anhui China The Georg-August University Goettingen Germany The Center for Molecular Microscopy Center for Cancer Research National Cancer Institute National Institutes of Health Bethesda United States The Cancer Research Technology Program Frederick National Laboratory for Cancer Research Frederick United States The Francis Crick Institute London United Kingdom The Advanced Biomedical Computational Science Group Frederick National Laboratory for Cancer Research FrederickMD United States The Computer Science Department Boston College Chestnut Hill MA United States

In this paper, we present the results of the MitoEM challenge on mitochondria 3D instance segmentation from electron microscopy images, organized in conjunction with the IEEE-ISBI 2021 conference. Our benchmark dataset consists of two large-scale 3D volumes, one from human and one from rat cortex tissue, which are 3,600 times larger than previously used datasets. At the time of paper submission, 257 participants had registered for the challenge, 14 teams had submitted their results, and six teams participated in the challenge workshop. Here, we present eight top-performing approaches from the challenge participants, along with our own baseline strategies. Posterior to the challenge, annotation errors in the ground truth were corrected without altering the final ranking. Additionally, we present a retrospective evaluation of the scoring system which revealed that (1) the challenge metric was permissive with the false positive predictions and (2) the size-based grouping of instances did not correctly categorize mitochondria of interest. Thus, we propose a new scoring system that better reflects the correctness of the segmentation results. Although several of the top methods are compared favorably to our own baselines, substantial errors remain unsolved for mitochondria with challenging morphologies. Thus, the challenge remains open for submission and automatic evaluation, with all volumes available for download. © 2023, CC BY.

关键词： Electron microscopy

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Geographic information science in the era of geospatial big data: A cyberspace perspective

引用

The Innovation 2022年第5期3卷 21-22页

作者： Xintao Liu Min Chen Christophe Claramunt Michael Batty Mei-Po Kwan Ahmad MSenousi Tao Cheng Josef Strobl Arzu Cöltekin John Wilson Temenoujka Bandrova Milan Konecny Paul MTorrens Fengyuan Zhang Li He Jinfeng Wang Carlo Ratti Olaf Kolditz Alexander Klippel Songnian Li Hui Lin Guonian Lu Department of Land Surveying and Geo-Informatics Hong Kong Polytechnic UniversityHong Kong SARKowloonChina Key Laboratory of Virtual Geographic Environment(Ministry of Education of PRC) Nanjing Normal UniversityNanjing 210023China The French Naval Academy Research Institute 29240 Lanveoc-PoulmicFrance The Bartlett Centre for Advanced Spatial Analysis(CASA) University College London(UCL)WC1E 6BT LondonUK Institute of Space and Earth Information Science The Chinese University of Hong KongHong Kong SARShatin 999077China Department of Civil Engineering Cairo University12613 CairoEgypt SpaceTimeLab Department of CivilEnvironmental and Geomatic EngineeringUniversity College London(UCL)WC1E 6BT LondonUK Department of Geoinformatics University of Salzburg5020 SalzburgAustria Institute of Interactive Technologies(IIT) University of Applied Sciences and Arts Northwestern Switzerland FHNW5210 WindischSwitzerland Spatial Sciences Institute University of Southern CaliforniaLos AngelesCA 90007USA Laboratory on Cartography Department of Photogrammetry and CartographyUniversity of ArchitectureCivil Engineering and Geodesy1164 SofiaBulgaria Laboratory on Geoinformatics and Cartography Department of GeographyMasaryk University61137 BrnoCeskáRepublika Computer Science and Engineering Tandon School&Center for Urban Science+ProgressNew York UniversityNew YorkNY 10012USA School of Humanities and Social Science Xi’an Jiaotong UniversityXi’an 710049China Institute of Geographic Sciences and Natural Resources Research Chinese Academy of SciencesBeijing 100101China Department of Urban Studies and Planning Massachusetts Institute of TechnologyCambridgeMA 02139USA Centre for Environmental Research Helmholtz Centre for Environmental Research-UFZ04318 LeipzigGermany Laboratory of Geo-information Science and Remote Sensing Wageningen University&ResearchWageningen 6708the Netherlands Department of Civil Engineering Toronto Metropolitan UniversityTorontoON M5B 2K3Canada School of Geography and Env

The advent of information and communication technology and the Internet of Things have led our society toward a digital *** proliferation of personal computers,smartphones,intelligent autonomous sensors,and pervasive network interactions with individuals have gradually shifted human activities from offline to online and from in person to *** transformation has brought a series of challenges in a variety of fields,such as the dilemma of placelessness,some aspects of timelessness(no time relevance),and the changing relevance of distance in the field of geographic information science(GIScience).In the last two decades,“cyber thinking”in GIScience has received significant attention from different *** instance,human activities in“cyberspace”need to be reconsidered when coupled with the geographic space to observe the first law of geography.

关键词： computer cyber instance

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Lesionmix Data Enhancement and Entropy Minimization for Semi-Supervised Lesion Segmentation of Lung Cancer

SSRN

引用

SSRN 2024年

作者： Pan, Xipeng Chen, Mingwei Lin, Huan Bian, Xinjun Feng, Siyang Chen, Jiale Wang, Lin Chen, Xin Liu, Zaiyi Lan, Rushi School of Computer Science and Information Security Guilin University of Electronic Technology Guangxi Guilin541004 China Department of Radiology Guangdong Provincial People’s Hospital Guangdong Academy of Medical Sciences Southern Medical University Guangzhou510080 China Guangdong Provincial Key Laboratory of Artificial Intelligence in Medical Image Analysis and Application Guangdong Provincial People’s Hospital Guangdong Academy of Medical Sciences Guangdong Guangzhou510080 China State Key Laboratory of Oncology in South China Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy Guangdong Provincial Clinical Research Center for Cancer Sun Yat-sen University Cancer Center Guangzhou510060 China Department of Nasopharyngeal Carcinoma Sun Yat-sen University Cancer Center Guangzhou510060 China Department of Radiology Guangzhou First People’s Hospital School of Medicine South China University of Technology Guangdong Guangzhou510180 China Guangdong Provincial People's Hospital China School of Medicine China

Determining the location and contour of the lesion is an important prerequisite for medical diagnosis, subsequent personalized treatment plan and prognostic prediction. Semi-supervised learning and data enhancement methods facilitate deep learning to be used in many fields of medical imaging. In this paper, we propose a data enhancement method named LesionMix, which performs lesion extraction and reuses through a small amount of labeled CT data to improve the utilization efficiency of the labeled data. Meanwhile, we propose a two-stage semi-supervised training strategy called Entropy Minimization LesionMix, in which features containing lesion contour information are quickly learned through LesionMix data augmentation in the first stage. Entropy minimization strategy optimizes the model parameters to alleviate overfitting as much as possible in the second stage and improves prediction confidence. Our proposed method is validated on an public LIDC-IDRI dataset and an in-house GDPHLUAD dataset. Extensive experiments demonstrate that our method achieves promising performance and outperforms seven state-of-the-art semi-supervised models;Moreover, ablation experiments validate the effectiveness of various aspects of our approach. © 2024, The Authors. All rights reserved.

关键词： Diseases

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Hypercomplex Low Rank Reconstruction for Nmr Spectroscopy with Cloud Computing ⋆

SSRN

引用

SSRN 2022年

作者： Guo, Yi Zhan, Jiaying Tu, Zhangren Zhou, Yirong Wu, Jianfan Hong, Qing Orekhov, Vladislav Qu, Xiaobo Guo, Di School of Computer and Information Engineering Fujian Engineering Research Center for Medical Data Mining and Application Xiamen University of Technology Xiamen361024 China Department of Electronic Science Biomedical Intelligent Cloud R&D Center Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance Xiamen University Xiamen361005 China China Mobile Group Xiamen361005 China Swedish NMR Center Department of Chemistry and Molecular Biology University of Gothenburg Gothenburg41390 Sweden

Nuclear magnetic resonance (NMR) spectroscopy serves as an important tool to analyze chemicals and proteins in bioengineering. Multi-dimensional NMR offers a major improvement in resolution with multi-dimensional spectrum, but significantly increases data acquisition time and produces hypercomplex data that is difficult to be handled. To reduce this time, non-uniformly sampling can be applied to obtain undersampled data and using a reconstruction approach, such as the state-of-the-art low-rank method, to remove the spectral artifacts introduced by undersampling. However, only complex format of signal, including the real and imaginary parts, is considered in previous low-rank approach, which is less efficient when dealing with hypercomplex data that has multiple components. To deal with this problem, a hypercomplex low-rank model is proposed by introducing an adjoint matrix operation and then solved with a fast matrix factorization algorithm. This method efficiently uses redundant information among all the components of hypercomplex signal. Using simulated data and real protein data, we demonstrate that the proposed method provides a fast and high-fidelity reconstruction of hypercomplex NMR spectroscopy. Furthermore, an open-access and easy-to-use cloud-computing platform is developed for this method. © 2022, The Authors. All rights reserved.

关键词： Nuclear magnetic resonance spectroscopy

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A convolutional neural network-based diagnostic method using resting-state electroencephalograph signals for major depressive and bipolar disorders

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Biomedical Signal Processing and Control 2022年第PartB期72卷 103370-103370页

作者： Lei, Yu Belkacem, Abdelkader Nasreddine Wang, Xiaotian Sha, Sha Wang, Changming Chen, Chao Beijing Institute of Basic Medical Sciences Beijing China Department of Computer and Network Engineering College of Information Technology United Arab Emirates University Al Ain United Arab Emirates School of Artificial Intelligence Xidian University Xian China National Clinical Research Center for Mental Disorders & Beijing Key Laboratory of Mental Disorders Beijing Anding Hospital Capital Medical University Beijing China Brain-inspired Intelligence and Clinical Translational Research Center/Department of Neurosurgery Xuanwu Hospital Capitap Medical University Beijing China Key Laboratory of Complex System Control Theory and Application Tianjin University of Technology China Academy of Medical Engineering and Translational Medicine Tianjin University Tianjin China

Background: Early and accurate diagnosis of bipolar and major depressive disorders is important in clinical practice. However, no diagnostic biomarkers can discriminate bipolar from major depressive disorder with high accuracy at present. Methods: We propose a novel convolutional neural network architecture using multichannel raw resting-state electroencephalograph signals to differentiate bipolar disorder from major depressive disorder. This method has great potential in diagnosing mental disorders. In total, 101 patients with major depressive disorder, 82 patients with bipolar disorder, and 81 healthy controls were assessed. Clinical diagnosis was performed by psychiatrists based on the Diagnostic and Statistical Manual of Mental Disorders, fifth edition. Participants were instructed to fix their eyes on a cross on the monitor during the collection of resting-state electroencephalograph signals. Results: A classification mean accuracy of 96.88% was achieved using the resting-state electroencephalograph signals with the 10-fold cross-validation method. The results indicate that deep neural networks could learn efficient feature patterns automatically without manual feature selections. Both statistical analysis and feature visualization on different brain regions showed that the classification performance and the learned features of the proposed model were consistent with that obtained in neurobiological studies on bipolar and major depressive disorders. Conclusions: The combined use of deep neural networks and electroencephalograph signals is an effective approach for the computer-aided diagnosis of bipolar and major depressive disorders. © 2021 Elsevier Ltd

关键词： Deep neural networks

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Prototype Learning Guided Hybrid Network for Breast Tumor Segmentation in DCE-MRI

arXiv

引用

arXiv 2024年

作者： Zhou, Lei Zhang, Yuzhong Zhang, Jiadong Qian, Xuejun Gong, Chen Sun, Kun Ding, Zhongxiang Wang, Xing Li, Zhenhui Liu, Zaiyi Shen, Dinggang The School of Health Science and Engineering University of Shanghai for Science and Technology Shanghai China The School of Biomedical Engineering ShanghaiTech University China The School of Computer Science and Engineering Nanjing University of Science and Technology China Ruijin Hospital Shanghai Jiaotong University School of Medicine China Department of Radiology Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province China The Shanghai General Hospital Shanghai JiaoTong University China Department of Radiology The Third Affiliated Hospital of Kunming Medical University China Department of Radiology Guangdong Provincial Peo-ple's Hospital Guangdong Academy of Medical Sciences Guangzhou510080 China Guangdong Provincial Key Laboratory of Artificial Intelligence in Medical Image Analysis and Application Guangdong Provincial People's Hospital Guangdong Academy of Medical Sciences Guangzhou510080 China School of Biomedical Engineering State Key Laboratory of Advanced Medical Materials and Devices ShanghaiTech University Shanghai201210 China Shanghai United Imaging Intelligence Co. Ltd. Shanghai200232 China Shanghai Clinical Research and Trial Center Shanghai201210 China

Automated breast tumor segmentation on the basis of dynamic contrast-enhancement magnetic resonance imaging (DCE-MRI) has shown great promise in clinical practice, particularly for identifying the presence of breast disease. However, accurate segmentation of breast tumor is a challenging task, often necessitating the development of complex networks. To strike an optimal tradeoff between computational costs and segmentation performance, we propose a hybrid network via the combination of convolution neural network (CNN) and transformer layers. Specifically, the hybrid network consists of a encoder-decoder architecture by stacking convolution and deconvolution layers. Effective 3D transformer layers are then implemented after the encoder subnetworks, to capture global dependencies between the bottleneck features. To improve the efficiency of hybrid network, two parallel encoder subnetworks are designed for the decoder and the transformer layers, respectively. To further enhance the discriminative capability of hybrid network, a prototype learning guided prediction module is proposed, where the category-specified prototypical features are calculated through online clustering. All learned prototypical features are finally combined with the features from decoder for tumor mask prediction. The experimental results on private and public DCE-MRI datasets demonstrate that the proposed hybrid network achieves superior performance than the state-of-the-art (SOTA) methods, while maintaining balance between segmentation accuracy and computation cost. Moreover, we demonstrate that automatically generated tumor masks can be effectively applied to identify HER2-positive subtype from HER2-negative subtype with the similar accuracy to the analysis based on manual tumor segmentation. The source code is available at https://***/ZhouLlab/PLHN. Copyright © 2024, The Authors. All rights reserved.

关键词： Multilayer neural networks

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