Article
Chemistry, Multidisciplinary
Eric Schwenker, Venkata Surya Chaitanya Kolluru, Jinglong Guo, Rui Zhang, Xiaobing Hu, Qiucheng Li, Joshua T. Paul, Mark C. Hersam, Vinayak P. Dravid, Robert Klie, Jeffrey R. Guest, Maria K. Y. Chan
Summary: This paper introduces an open-source automation framework called ingrained, which solves the correspondence between simulation and experimental images and fuses atomic resolution image simulations into the corresponding experimental images.
Article
Optics
Mengnan Liu, Yu Han, Xiaoqi Xi, Linlin Zhu, Huijuan Fu, Siyu Tan, Xiangzhi Zhang, Lei Li, Jian Chen, Bin Yan
Summary: Nanocomputed tomography is an effective tool for observing 3D structures of nanomaterials, but it requires correction phantom to reduce artifacts. This study proposes a rough-to-refined correction framework based on global mixed evaluation for precise drift estimation.
Article
Biochemical Research Methods
Ruohua Shi, Keyan Bi, Kai Du, Lei Ma, Fang Fang, Lingyu Duan, Tingting Jiang, Tiejun Huang
Summary: Cell membrane segmentation in electron microscopy (EM) images is an important task. Current approaches perform well on low-resolution datasets but struggle with high-resolution datasets. Through eye movement and perceptual consistency experiments, we found that humans are more sensitive to membrane structure and can tolerate misalignment. Based on these findings, we propose a computational framework that incorporates human perception characteristics, including the perceptual Hausdorff distance (PHD) evaluation metric and a PHD-guided segmentation network (PS-Net).
Article
Biochemical Research Methods
Fangxu Zhou, Lijun Shen, Bohao Chen, Xi Chen, Han Hua
Summary: In this research, a spatial attention-based registration method for serial EM images was developed to improve alignment accuracy. By combining the U-Net framework with STN networks and incorporating a SA module, the approach achieved state-of-the-art results in terms of accuracy and provided smooth and reliable transformations for image stack restoration.
Article
Neurosciences
Fangxu Zhou, Bohao Chen, Xi Chen, Hua Han
Summary: This paper presents a new method for serial section image registration by utilizing a neuronal morphological model and combining feature extraction with global optimization. The proposed method achieves more reasonable and reliable registration results compared to existing approaches.
FRONTIERS IN HUMAN NEUROSCIENCE
(2022)
Article
Computer Science, Theory & Methods
Marcin Copik, Tobias Grosser, Torsten Hoefler, Paolo Bientinesi, Benjamin Berkels
Summary: This article studies the recursive registration of electron microscopy images and converts it into a parallel computation using a suitable prefix scan algorithm, significantly reducing the time-to-solution.
IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS
(2022)
Article
Chemistry, Medicinal
Yu-Xuan Chen, Rui Xie, Yang Yang, Lin He, Dagan Feng, Hong-Bin Shen
Summary: This paper introduces a new algorithm for two-dimensional pairwise alignment of cryo-EM particle images, which improves the precision of image distance calculation. Compared to existing methods, this algorithm directly computes alignment parameters using signal distribution and feature on the images' power spectrum, without requiring iterative computations and being robust against noise.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Engineering, Biomedical
Marek Wodzinski, Andrzej Skalski
Summary: The use of multiple dyes in histological sample preparation can reveal distinct tissue properties, but nonrigid image registration is necessary due to deformations caused by slide preparation differences. A multistep, automatic method was proposed for such image registration challenges, achieving competitive results in the ANHIR dataset evaluation with high reproducibility and no need for manual interaction.
PHYSICS IN MEDICINE AND BIOLOGY
(2021)
Correction
Engineering, Electrical & Electronic
Amit Lal, Chunyan Sha, Peng Xi
Summary: This article presents corrections to the paper "Structured Illumination Microscopy Image Reconstruction Algorithm".
IEEE JOURNAL OF SELECTED TOPICS IN QUANTUM ELECTRONICS
(2023)
Article
Computer Science, Artificial Intelligence
Sehyung Lee, Hideaki Kume, Hidetoshi Urakubo, Haruo Kasai, Shin Ishii
Summary: The paper proposes a novel approach for restoring the image quality of three-dimensional neural imaging using convolutional neural networks. By estimating and fusing the intersection regions of images captured from three orthogonal viewpoints, the method improves the image quality along the depth direction and enhances the identification of neural connectivity.
Review
Biology
Hanguang Xiao, Xufeng Xue, Mi Zhu, Xin Jiang, Qingling Xia, Kai Chen, Huanqi Li, Li Long, Ke Peng
Summary: This review discusses the development and applications of lung image registration, with a focus on deep learning-based methods and their different supervision types. The review also provides a comprehensive analysis of evaluation metrics, loss functions, and publicly available datasets for lung image registration.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Computer Science, Artificial Intelligence
Ruixing Zhang, Tao Yao, Lianshan Yan
Summary: This paper proposes a self-supervised feature point detection and description network called ACPoint, which uses an asymmetric convolution module to train three convolution branches simultaneously. It enhances the backbone of the square convolution from both horizontal and vertical directions to improve the representation of local features. Based on the ACPoint network, a cross-resolution image-matching method is proposed. Experimental results show that the proposed network model achieves higher localization accuracy and homography estimation ability on the HPatches dataset.
INTERNATIONAL JOURNAL OF INTELLIGENT SYSTEMS
(2023)
Article
Computer Science, Artificial Intelligence
Paul Striewski, Benedikt Wirth
Summary: This paper proposes a method for nonrigidly aligning a 3D volumetric image with a 2D planar image for biological studies. By co-registering the 2D intravital microscopy videos with the more detailed 3D volume microscopy data after tissue excision, both temporal and spatial information can be combined.
JOURNAL OF MATHEMATICAL IMAGING AND VISION
(2022)
Article
Materials Science, Multidisciplinary
Chenyu Zhang, Jie Feng, Andrew B. Yankovich, Alexander Kvit, Benjamin Berkels, Paul M. Voyles
Summary: Achieving sub-picometer precision measurements of atomic column positions in high-resolution scanning transmission electron microscope images using nonrigid registration (NRR) and averaging of image series requires careful optimization of experimental conditions and algorithm parameters. Sub-pm precision on experimental data from SrTiO3 [100] demands alignment to the zone axis, minimal tilt, and sample drift, while the smoothness factor within the NRR algorithm plays a crucial role in determining sub-pm precision.
MICROSCOPY AND MICROANALYSIS
(2021)
Review
Physiology
Kenneth W. Dunn
Summary: Over the past 30 years, the scale and complexity of images collected in biological microscopy have grown enormously. The development of multiphoton microscopy and new methods of optical sectioning and tissue clearing have provided biologists with the ability to characterize entire organs at subcellular resolution. The Indiana O'Brien Center has been developing robust and accessible image analysis tools for biomedical researchers to utilize these advanced imaging techniques.
FRONTIERS IN PHYSIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Maxime Taquet, Stephen M. Smith, Anna K. Prohl, Jurriaan M. Peters, Simon K. Warfield, Benoit Scherrer, Paul J. Harrison
Summary: Psychiatry is shifting from accepting distinct diagnoses to a representation of psychiatric illness that crosses diagnostic boundaries. A study shows that the brain vulnerability network may form a common neurobiological root for different psychiatric disorders, funneling genetic risks through shared neurobiological mechanisms.
MOLECULAR PSYCHIATRY
(2021)
Article
Radiology, Nuclear Medicine & Medical Imaging
Tess E. Wallace, Jonathan R. Polimeni, Jason P. Stockmann, W. Scott Hoge, Tobias Kober, Simon K. Warfield, Onur Afacan
Summary: This study developed a method for slice-wise dynamic distortion correction for EPI using FID navigators and demonstrated its efficacy relative to an established data-driven technique. Results showed that the FID-navigated distortion correction accurately corrected image geometry in the presence of induced magnetic field perturbations and yielded significant temporal SNR gains in functional MRI scans.
MAGNETIC RESONANCE IN MEDICINE
(2021)
Article
Computer Science, Artificial Intelligence
Jaume Coll-Font, Onur Afacan, Jeanne S. Chow, Richard S. Lee, Simon K. Warfield, Sila Kurugol
Summary: Early identification of kidney function deterioration in newborns with congenital kidney disease is crucial for determining surgical intervention. However, motion artifacts in DCE-MR imaging can introduce errors in tracer kinetic model estimation. A novel LTI model is proposed to improve registration stability and accuracy, showing promising results in aligning volumes and fitting the tracer kinetic model.
MEDICAL IMAGE ANALYSIS
(2021)
Article
Clinical Neurology
F. Machado-Rivas, O. Afacan, S. Khan, B. Marami, C. K. Rollins, C. Ortinau, C. Velasco-Annis, S. K. Warfield, A. Gholipour, C. Jaimes
Summary: A new algorithm enabled real-time tracking of developmental changes in the cerebellar peduncles and revealed significant alterations in various metrics as gestational age increased.
AMERICAN JOURNAL OF NEURORADIOLOGY
(2021)
Article
Radiology, Nuclear Medicine & Medical Imaging
Jaume Coll-Font, Onur Afacan, Scott Hoge, Harsha Garg, Kumar Shashi, Bahram Marami, Ali Gholipour, Jeanne Chow, Simon Warfield, Sila Kurugol
Summary: DW-MRI of the kidneys can provide information about renal tissue microstructure, but physiological motion and main B-0 field inhomogeneities can lead to large geometric distortions, reducing image quality and quantitative imaging marker accuracy.
JOURNAL OF MAGNETIC RESONANCE IMAGING
(2021)
Article
Neurosciences
Fedel Machado-Rivas, Onur Afacan, Shadab Khan, Bahram Marami, Clemente Velasco-Annis, Hart Lidov, Simon K. Warfield, Ali Gholipour, Camilo Jaimes
Summary: Population averaged diffusion atlases can be used to characterize complex microstructural changes with less bias compared to individual data. In this study, a fetal DTI atlas was used to investigate tract-based changes in anisotropy and diffusivity during gestational age, revealing tract-specific, nonlinear changes related to age and significant heterogeneity within tracts like CST, IFOF, and forceps major.
HUMAN BRAIN MAPPING
(2021)
Article
Computer Science, Interdisciplinary Applications
Arvind Balachandrasekaran, Alexander L. Cohen, Onur Afacan, Simon K. Warfield, Ali Gholipour
Summary: Functional MRI (fMRI) is widely used for studying the functional organization of the brain, but the signal can be contaminated by subject motion artifacts. This study proposes a new approach to recover the censored fMRI signal using structured low rank matrix completion, reducing the adverse effects of motion in fMRI analysis.
IEEE TRANSACTIONS ON MEDICAL IMAGING
(2022)
Article
Computer Science, Interdisciplinary Applications
Yao Sui, Onur Afacan, Camilo Jaimes, Ali Gholipour, Simon K. Warfield
Summary: High spatial resolution is important for the interpretation and analysis of Magnetic Resonance Imaging (MRI), but direct acquisition is time-consuming and costly. Super-resolution reconstruction (SRR) allows for a balance between high spatial resolution, high signal-to-noise ratio (SNR), and reduced scan times. Deep learning has improved SRR, but requires large-scale training datasets of high-resolution images. We developed a dataset-free learning method using generative neural networks for tailored SRR. With three short duration scans, we achieved high-quality brain MRI with enhanced spatial resolution and SNR. Our approach outperformed state-of-the-art methods while reducing costs.
IEEE TRANSACTIONS ON MEDICAL IMAGING
(2022)
Article
Radiology, Nuclear Medicine & Medical Imaging
Fedel Machado-Rivas, Jasmine Gandhi, Jungwhan John Choi, Clemente Velasco-Annis, Onur Afacan, Simon K. Warfield, Ali Gholipour, Camilo Jaimes
Summary: This study used a spatiotemporal MRI atlas to evaluate the volumetric growth of intracranial structures in healthy fetuses, taking into account gestational age, sex, and laterality. The results showed that the volumetric growth of the fetal brain exhibited complex trajectories dependent on structure, gestational age, sex, and laterality.
Article
Radiology, Nuclear Medicine & Medical Imaging
Tess E. Wallace, Tobias Kober, Jason P. Stockmann, Jonathan R. Polimeni, Simon K. Warfield, Onur Afacan
Summary: In this study, a method for real-time field control using rapid FID navigator measurements was implemented, and its effectiveness in mitigating dynamic field perturbations and improving image quality was evaluated. The results showed that real-time shimming with FID navigator successfully compensated for field offsets and reduced field fluctuations, leading to an improvement in image quality.
MAGNETIC RESONANCE IN MEDICINE
(2022)
Article
Neurosciences
Benjamin F. Zwick, George C. Bourantas, Saima Safdar, Grand R. Joldes, Damon E. Hyde, Simon K. Warfield, Adam Wittek, Karol Miller
Summary: Invasive intracranial electroencephalography (iEEG) or electrocorticography (ECoG) can be used for epilepsy surgery planning, but accurate solution of the forward problem requires accurate representation of patient's brain geometry and tissue conductivity after electrode implantation. A biomechanics-based image warping procedure using preoperative MRI and postoperative CT allows non-rigid registration of preoperative image data to postoperative configuration, enabling accurate solution of the iEEG forward problem on deformed brain geometry.
Article
Multidisciplinary Sciences
Arka N. Mallela, Hansen Deng, Ali Gholipour, Simon K. Warfield, Ezequiel Goldschmidt
Summary: The human cerebrum has a specific arrangement of lobes, primary gyri, and connectivity that underlies cognition. The development of this arrangement is not well understood, and current models do not explain the global configuration of the cerebral lobes. The insula, a part of the cerebrum buried in the Sylvian fissure, has unique morphology and location. This study quantitatively examines the unique development of the insula and identifies differences in migration patterns that may explain these unique characteristics.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Radiology, Nuclear Medicine & Medical Imaging
Tess E. Wallace, Davide Piccini, Tobias Kober, Simon K. Warfield, Onur Afacan
Summary: This study aims to develop a self-navigated motion compensation strategy for 3D radial MRI, which can compensate for continuous head motion by measuring rigid body motion parameters from the central k-space acquisition point. The results show that self-encoded FID navigators can accurately obtain rigid body motion parameters and substantially improve image quality through retrospective correction. This approach is suitable for subjects with frequent head motion.
MAGNETIC RESONANCE IN MEDICINE
(2023)
Article
Computer Science, Artificial Intelligence
Serge Didenko Vasylechko, Simon K. Warfield, Sila Kurugol, Onur Afacan
Summary: We present a generative model for synthesizing large-scale 3D datasets for quantitative mapping of myelin water fraction (MWF). Our model combines MR physics signal decay model with a probabilistic multi-component T2 model, and can be used to train CNN models for MWF estimation. Experimental results show that our synthetically trained CNN achieves superior accuracy compared to competing methods.
MEDICAL IMAGE ANALYSIS
(2024)
Proceedings Paper
Computer Science, Artificial Intelligence
Noam Korngut, Elad Rotman, Onur Afacan, Sila Kurugol, Yael Zaffrani-Reznikov, Shira Nemirovsky-Rotman, Simon Warfield, Moti Freiman
Summary: The SUPER-IVIM-DC method introduced in this study enables IVIM analysis of DWI data with a limited number of b-values, reducing the long acquisition times associated with this analysis. This method provides clinically feasible biomarkers for non-invasive fetal lung maturity assessment.
MEDICAL IMAGE COMPUTING AND COMPUTER ASSISTED INTERVENTION, MICCAI 2022, PT II
(2022)