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Eff-SAM: SAM-based Efficient Method for Brain Tumor Segmentation in Multimodal 3D MRI Scans

IEEE Access 2025年 13卷 90063-90087页

作者： Ahmad, Nisar Chen, Yao-Tien Ming Chi University of Technology International Ph.D. Program in Innovative Technology of Biomedical Engineering Medical Devices New Taipei City243303 Taiwan

Accurate brain tumor segmentation in MRI scans is crucial for effective diagnosis and treatment planning, as even minor segmentation errors can lead to significant clinical concerns. However, this task is challenged by the complex anatomy of the brain, variable tumor shapes, and low contrast between tumor sub-regions. Moreover, existing methods often lack generalizability across diverse segmentation tasks and imaging modalities. Large Vision Model (LVM) like the Segment Anything Model (SAM) represents a foundational advancement in tumor segmentation. While SAM has shown impressive performance on natural images, its effectiveness in medical imaging, especially brain tumor segmentation, is limited due to domain differences and indistinct boundaries in MRI scans. To address these challenges, we propose Eff-SAM, a 3D brain tumor segmentation framework that adapts SAM for medical applications through Parameter-Efficient Fine-Tuning (PEFT) technique. The framework incorporates PEFT with adapters into SAM’s encoder to fine-tune the model effectively and optimize its performance for medical imaging while maintaining computational efficiency. Additionally, a Cross-Sliced Attention (CSA) mechanism captures semantic relationships, improves tumor localization, and is introduced into the encoder. Robust data preprocessing further enhances the model’s generalization across datasets. Eff-SAM demonstrates state-of-the-art performance and outperforms benchmark methods on the BraTS 2020 and BraTS 2021 datasets. It achieves Dice scores of 0.884 for Whole Tumor (WT), 0.853 for Tumor Core (TC), and 0.818 for Enhancing Tumor (ET) on the BraTS 2020 dataset, and 0.880 (WT), 0.861 (TC), and 0.821 (ET) on the BraTS 2021 dataset. This work highlights the potential of integrating vision models like SAM with lightweight, domain-specific modules to deliver accurate and efficient brain tumor segmentation offering a clinically valuable tool, especially in scenarios with limited data and complex tu

关键词： Semantic Segmentation

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Computational Modeling of the Pendulum Test to Simulate Spasticity in the Elbow Joint 9th

Computational Modeling of the Pendulum Test to Simulate Spas...

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9th Latin American Congress on biomedical engineering, CLAIB 2022 and 28th Brazilian Congress on biomedical engineering, CBEB 2022

作者： Pasqualin, B.R. Silva, V.A. Orselli, M.I.V. Manffra, E.F. Pontifícia Universidade Católica do Paraná Biomedical Engineering Curitiba Brazil Pontifícia Universidade Católica do Paraná Postgraduate Program in Health Technology Curitiba Brazil Instituto Vita São Paulo Brazil

ISBN: (纸本)9783031494062

Computational models have been developed to help understand phenomena such as spasticity. In this study, we aim to develop a computational model using the Matlab-OpenSim interface to simulate the passive pendulum test in the elbow joint and evaluate whether the input of a neural excitation pattern with spasticity in the model would be sufficient to reproduce an altered kinematic pattern during an elbow pendulum test. We built a model with two segments that represent the humerus and radius bones, added two actuators to represent the biceps and triceps muscles, and the excitation values were obtained from the electromyography signal available in the literature. For the first simulation we used the electromyography (EMG) signal from a non-spastic person and for the last simulation was used the excitation values from a person with mild spasticity. Our results showed that it is possible to reproduce the pendulum test at the elbow joint, but modifications in the model are necessary to better reproduce the movement. © 2024, The Author(s), under exclusive license to Springer Nature Switzerland AG.

关键词： MATLAB

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Characterization of Electroencephalography (EEG) Responses to Musical Stimuli 3

Characterization of Electroencephalography (EEG) Responses t...

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3rd International Congress of biomedical engineering and Bioengineering, CIIBBI 2024

作者： Rojas Tocora, Angelica Maria Muller, Oliver Orjuela-Canon, Alvaro D. Ortiz, Victor A. Universidad Del Rosario - Escuela Colombiana de Ingeniería Biomedical Engineering Program Julio Garavito D.C. Bogota Colombia School of Medicine and Health Sciences Universidad Del Rosario D.C. Bogota Colombia Unversidad Tecnologica de Pereira Engineering Faculty Pereira Colombia

ISBN: (纸本)9798331532352

This study investigates the effects of different musical genres on electroencephalographic (EEG) responses in healthy subjects. The EEG technique was analyzed for five different music styles, such as classical, rock, jazz, vallenato, and urban, and in this way, to determine the influence in brainwave patterns. For instance, classical music was linked to alpha brainwave patterns associated with relaxation, while genres like rock and reggaeton are associated with beta patterns, indicating of concentration and mental activity. The study also explores how intrinsic factors such as musical lyrics and individual differences like musical training and preferences impact brain activity. Findings suggest that music can evoke strong emotional responses and activate different brain regions depending on the genre and individual factors. This complexity underscores the importance of considering personal and cultural aspects in understanding the neural dynamics of musical experiences. © 2024 IEEE.

关键词： Electrophysiology

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Investigating the effect of cerebral atrophy on brain deformation using subject-specific models

Investigating the effect of cerebral atrophy on brain deform...

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Medical Imaging 2023: biomedical Applications in Molecular, Structural, and Functional Imaging

作者： Hong, Allen Carass, Aaron Zuo, Lianrui Prince, Jerry L. Alshareef, Ahmed Department of Biomedical Engineering The College of New Jersey EwingNJ08618 United States Department of Electrical and Computer Engineering Johns Hopkins University BaltimoreMD21218 United States Laboratory of Behavioral Neuroscience National Institute on Aging National Institutes of Health BaltimoreMD20892 United States Biomedical Engineering Program University of South Carolina ColumbiaSC29208 United States

ISBN: (纸本)9781510660410

Traumatic brain injuries (TBIs) are a major health risk that increases with age. Natural brain aging results in cerebral atrophy and the enlargement of the ventricular regions. The objective of this study is to investigate the effect of cerebral atrophy on brain biomechanics with subject-specific models to determine the risk of traumatic brain injury (TBI). Utilizing subjects from a longitudinal study of aging in healthy volunteers, we created subject-specific brain models of a small cohort with progressive age-related cerebral atrophy. We then simulate concussive loading conditions to study changes in brain deformation, a correlate to risk of TBI. The results display differing trends with increasing ventricle volume, with some subjects exhibiting increases and others showing decreasing strain. Additional subject simulations are needed to clarify these the causes of these trends. © COPYRIGHT SPIE. Downloading of the abstract is permitted for personal use only.

关键词： Health risks

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Foot hemodynamics using optical tomography: A potential biomarker of peripheral arterial disease

Foot hemodynamics using optical tomography: A potential biom...

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2023 Advances in Science and engineering Technology International Conferences, ASET 2023

作者： Al Abdi, Rabah M. Zakaria, Amer Al Nashash, Hasan Zalak, Tasnim Goswami, Nandu Jeet, Vishwa Jordan Univ. of Science and Tech. Dept. of Biomedical Engineering Irbid Jordan American University of Sharjah Dept. of Electrical Engineering Sharjah United Arab Emirates American University of Sharjah Master of Science in Biomedical Engineering Program Sharjah United Arab Emirates College of Medicine Mohammed Bin Rashed University of Medicine and Health Sciences Dubai United Arab Emirates

ISBN: (纸本)9781665454742

Peripheral arterial disease (PAD) is the narrowing of the arteries within the lower extremities, which inhibits blood flow to the foot. We present the use of dynamic diffuse optical tomography (DDOT) system to measure blood flow in the foot during venous and arterial occlusions. DDOT is a non-ionizing, contrast-free, and fast imaging modality. The DDOT system consists of 4 sensors, each containing four laser diodes (at wavelengths of 670, 780, 808, and 850 nm) and two silicon photodiodes. We examined 11 healthy subjects with a protocol consisting of five consecutive measurements. Biomarkers were extracted from changes in hemoglobin concentrations during the measurements. The results from a pilot study are presented in this report. The average increase in total hemoglobin was 17.2 ±5.8 μ M during a measurement with 60 mmHg occlusion and 10.4 ± 6.7 μ M during a measurement with 180 mmHg occlusion. The biomarkers can quantify blood perfusion and oxygen consumption in the foot, and they have the potential to detect and monitor PAD. © 2023 IEEE.

关键词： Hemodynamics

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Design and Feasibility Test of In-House Indirect Perfusion Bioreactor for 3-D Cell Culture 15

Design and Feasibility Test of In-House Indirect Perfusion B...

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15th biomedical engineering International Conference, BMEiCON 2023

作者： Suwannaphan, T. Tharasanit, T. Wongpakham, T. Pimpin, A. Chessadangkul, K. King Mongkut's University of Technology North Bangkok Department of Mechanical Engineering Technology Bangkok Thailand Faculty of Veterinary Science Chulalongkorn University Department of Obstetrics Gynaecology and Reproduction Bangkok Thailand Chulalongkorn University Faculty of Engineering Department of Mechanical Engineering Bangkok Thailand Chulalongkorn University Biomedical Engineering Program Faculty of Engineering Bangkok Thailand

ISBN: (纸本)9798350345247

Selection of bioreactor system depends on many factors such as type of products, process of culture, and product density. No standard for development methodology is available nowadays. This work demonstrated the development of multi mini-chamber indirect perfusion bioreactor to support 3-D cell culture. The systems consisted of scaffolds, cell/scaffold retainers, culture tanks with a single peristaltic pump. Flow simulation was conducted to investigate the effects of flow rate and inlets/outlets' position on the distribution of shear stresses on the cell/scaffold cassettes installed inside the bioreactor. The prototype with 4 culture tanks connected in series was tested for long period operation. Lastly, preliminary experiments to culture and differentiate pig muscle stem cells were conducted. The results showed that muscle cells were successfully differentiated both on glass slides and aloe vera scaffolds inside the developed bioreactor. © 2023 IEEE.

关键词： Flow simulation

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Feasibility Study of Finger Interface for Miniature Surgical Instruments

Feasibility Study of Finger Interface for Miniature Surgical...

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Telepresence, IEEE Conference on

作者： Serin Cha Sebin Kim Seok Chang Ryu BioRobotics Laboratory Department of Mechanical and Biomedical Engineering Graduate Program in Smart Factory Ewha Womans University Seoul South Korea BioRobotics Laboratory Department of Mechanical and Biomedical Engineering Ewha Womans University Department of Mechanical and Biomedical Engineering BioRobotics Laboratory Ewha Womans University

ISBN: (数字)9798331528249

ISBN: (纸本)9798331528256

This paper presents a study on the design of a finger interface to improve the teleoperation of a miniaturized surgical instrument with a bendable distal section. A unique design principle employing the kinematic similarity between the human motion and the follower robot has been proposed for such instruments, which may result in embodied teleoperation, enhancing the overall telepresence experience. According to the principle, a design for an index finger interface was proposed, consisting of a sub-unit measuring finger motion and a handle. When the interface is connected to a robotic platform, it can control the entire tool motion in two separate ways: distal bending by the sub-unit and overall tool motion by the handle. A human subject test was conducted for trajectory-following tasks in a virtual environment, and their performance score was quantified for analysis of the learning curve. Based on the satisfactory learning rate of 75.78% for all nine subjects, the proposed finger interface could be a promising interface for a miniature surgical instrument with a long bendable section at the distal end.

关键词： Telepresence Instruments Fingers Virtual environments Kinematics Bending Motion measurement Robots

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Feasibility Study of a Teleoperation System With Haptics for Tip-Force Sensing Active Needles

Feasibility Study of a Teleoperation System With Haptics for...

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IEEE/RAS-EMBS International Conference on biomedical Robotics and Biomechatronics (BioRob)

作者： Sooyeon Kim Sujin Yu Yuri Lim Suhyun Lee Seok Chang Ryu Department of Mechanical and Biomedical Engineering BioRobotics Laboratory Graduate Program in Smart Factory Ewha Womans University Seoul South Korea Department of Mechanical and Biomedical Engineering BioRobotics Laboratory Ewha Womans University

ISBN: (数字)9798350386523

ISBN: (纸本)9798350386530

This paper presents the design of a teleoperation system with a haptic display for the active needles with tip-force sensing and tip-steering capabilities. The active needle design employs sensorized tendons by fiber Bragg gratings sensor (FBGs), while the teleoperation system combines a general haptic interface with electrical stimulation as its steering interface, delivering not only general force feedback but also tip-force information measured by the FBGs-based tendons to the operators. The essential features, such as tip-force sensing, teleoperation of the tip-joint, and human perception of the measured tip-force, were experimentally evaluated with their prototypes in tissue phantoms. Based on the results obtained, necessary follow-up studies were identified and suggested for the effective teleoperation of force-sensing steerable instruments in clinical environments. If successfully developed, such systems can enable surgeons to perceive clinical situations and perform operations more precisely and safely.

关键词： Instruments Surgery Prototypes Phantoms biomedical measurement Robot sensing systems Needles Fiber gratings Sensors Tendons

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Super-Resolution Displacement Spectroscopic Sensing over a Surface“Rainbow”

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engineering 2022年第10期17卷 75-81页

作者： Lyu Zhou Nan Zhang Chang Chieh Hsu Matthew Singer Xie Zeng Yizheng Li Haomin Song Josep Jornet Yun Wu Qiaoqiang Gan Department of Electrical Engineering The State University of New York at BuffaloBuffaloNY 14260USA Department of Biomedical Engineering The State University of New York at BuffaloBuffaloNY 14260USA Department of Electrical and Computer Engineering Northeastern UniversityBostonMA 02115USA Material Science Engineering Program King Abdullah University of Science and TechnologyThuwal 23955-6900Saudi Arabia

Subwavelength manipulation of light waves with high precision can enable new and exciting applications in spectroscopy,sensing,and medical *** these applications,miniaturized spectrometers are desirable to enable the on-chip analysis of spectral *** particular,for imaging-based spectroscopic sensing mechanisms,the key challenge is to determine the spatial-shift information accurately(i.e.,the spatial displacement introduced by wavelength shift or biological or chemical surface binding),which is similar to the challenge presented by super-resolution ***,we report a unique"rainbow"trapping metasurface for on-chip spectrometers and *** with super-resolution image processing,the low-setting 4×optical microscope system resolves a displacement of the resonant position within 35 nm on the plasmonic rainbow trapping metasurface with a tiny area as small as0.002 *** unique feature of the spatial manipulation of efficiently coupled rainbow plasmonic resonances reveals a new platform for miniaturized on-chip spectroscopic analysis with a spectral resolution of 0.032 nm in wavelength *** this low-setting 4×microscope imaging system,we demonstrate a biosensing resolution of 1.92×109exosomes per milliliter for A549-derived exosomes and distinguish between patient samples and healthy controls using exosomal epidermal growth factor receptor(EGFR)expression values,thereby demonstrating a new on-chip sensing system for personalized accurate bio/chemical sensing applications.

关键词： Rainbow trapping Metasurface Surface plasmon polaritons Super-resolution displacement On-chip biosensing

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Noise Aware System Generative Model (NASGM) of PET: a deep learning-based model for PET image simulation with quantitative assessment

Noise Aware System Generative Model (NASGM) of PET: a deep l...

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Medical Imaging 2025: Physics of Medical Imaging

作者： Li, Suya Dutta, Kaushik Shoghi, Kooresh I. Mallinckrodt Institute of Radiology Washington University School of Medicine St. Louis United States Imaging Science Program McKelvey School of Engineering Washington University in St. Louis St. Louis United States Department of Biomedical Engineering Washington University in St Louis St. Louis United States

ISBN: (纸本)9781510685888

Positron emission tomography (PET) simulation is widely applied in the development and validation of image processing algorithms as well as the optimization of imaging protocols because of its reproducibility and ability to provide ground truth. However, the simulation of PET images is generally time and computationally intensive. Furthermore, the non-differentiable nature of stochastic forward projection and iterative image reconstruction algorithms hinders our access to the underlying object space. To address these issues, we develop a deep learning-based PET simulation method, the noise-aware system generative model (NASGM). Specifically, we introduce a novel dual-domain discriminator to build a conditional generative adversarial network that processes activity and attenuation maps as inputs and generates simulated PET images by learning various noise characteristics of simulated PET images for different acquisition times. To prepare the dataset, a publicly available PET/CT clinical dataset is utilized as activity and attenuation maps, and FAST-PET (fast analytical simulator of tracer-PET), an analytical PET simulation tool we developed, is applied to simulate PET images. Validations in terms of recovery coefficient and normalized mean absolute error show that the NASGM-generated images have the highest quantitative accuracy and noise levels most closely matching those of the traditionally simulated images compared to other networks. In conclusion, the proposed NASGM functions as an efficient PET simulator that models the entire PET imaging and reconstruction system using a differentiable neural network and bridges the gap between the object and the image domain. © 2025 SPIE.

关键词： Positron emission tomography

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