Article
Biology
Max Hahn, Christoffer Nord, Maria Eriksson, Federico Morini, Tomas Alanentalo, Olle Korsgren, Ulf Ahlgren
Summary: This study presents a simple approach to reconstruct antibody labeled cells within entire human organs with preserved organ context, demonstrating previously unrecognized features of human islet mass distribution and pathology in the pancreas. The method may be translated to essentially any antibody marker or organ system, providing valuable insights into pancreatic anatomy/pathophysiology and potentially revealing new information on diseases like type 2 diabetes.
COMMUNICATIONS BIOLOGY
(2021)
Article
Optics
Zoya Alam, Raju Poddar
Summary: Zebrafish, as a vertebrate model, is widely used in various fields. This study demonstrates the use of optical coherence tomography and optical coherence tomography angiography to image the developing zebrafish, allowing for detailed visualization of microstructures and microvasculature.
OPTICS AND LASERS IN ENGINEERING
(2022)
Article
Biology
Veronika Miskolci, Kelsey E. Tweed, Michael R. Lasarev, Emily C. Britt, Alex J. Walsh, Landon J. Zimmerman, Courtney E. McDougal, Mark R. Cronan, Jing Fan, John-Demian Sauer, Melissa C. Skala, Anna Huttenlocher
Summary: This study used two-photon imaging of autofluorescent metabolic coenzymes NAD(P)H and FAD to assess macrophage metabolism in the wound microenvironment. Results showed that inhibiting glycolysis led to a more oxidized intracellular redox state in macrophages, and infection and thermal injury induced a more oxidized redox state in wounded tissues. Kinetic analysis revealed a shift toward a more reduced redox state during tissue repair. Metformin improved tissue repair by reducing TNF alpha+ wound macrophages and making the intracellular redox state more reduced, while depletion of STAT6 impaired regeneration by increasing TNF alpha+ wound macrophages and making the redox state more oxidized. The study suggests that autofluorescence of NAD(P)H and FAD can be used to probe the temporal and spatial regulation of macrophage metabolism during tissue damage and repair.
Article
Optics
Daewoon Seong, Won Ki, Pilun Kim, Jaeyul Lee, Sangyeob Han, Soojin Yi, Hong Kyun Kim, Mansik Jeon, Jeehyun Kim
Summary: This study developed a virtual intraoperative OCT angiography integrated surgical microscope, which can simultaneously visualize the morphological tissue structure and microvasculature data of the surgical region, demonstrating its potential application in in vivo imaging and simulated surgeries of small animals.
OPTICS AND LASERS IN ENGINEERING
(2022)
Article
Biochemical Research Methods
Xiang Xiang, Weijian Gao, Yao Xu, Yiqing Zhang, Ting Lu, Shuqi Gan, Jing Huang, Ziling Li, Li Huang, Yonghua Liao, Limei Wang, Jian Zhang
Summary: In this study, the efficacy of phycocyanin in bone defect repairing was tested on a zebrafish skull defect model, and the evaluating process was monitored in vivo using optical coherence tomography (OCT). The results demonstrated that phycocyanin can effectively repair bone defects, but a high dosage may cause deformation of the skull.
JOURNAL OF BIOPHOTONICS
(2022)
Article
Gastroenterology & Hepatology
Macarena Pozo-Morales, Ines Garteizgogeascoa, Camille Perazzolo, Juhoon So, Donghun Shin, Sumeet Pal Singh
Summary: This study successfully observed the changes in hepatocyte calcium dynamics by taking advantage of the transparency of zebrafish larvae. The presence of calcium oscillations, waves, and spikes in vivo were demonstrated, and it was found that calcium waves are related to nutrition intake and negatively regulate starvation-induced lipid droplet accumulation.
Article
Biochemical Research Methods
Di Yang, Zhuoqun Yuan, Muyun Hu, Yanmei Liang
Summary: This paper presents the use of polarization-sensitive optical coherence tomography (PS-OCT) to image the zebrafish brain and monitor the recovery process of a head wound. The results demonstrate that introducing polarization information can display more features of the brain, and the density of pigment in the skull is a critical factor affecting polarization imaging.
JOURNAL OF BIOPHOTONICS
(2022)
Review
Endocrinology & Metabolism
Tomas Alanentalo, Max Hahn, Stefanie M. A. Willekens, Ulf Ahlgren
Summary: The exocrine-endocrine multipart organization of the pancreas presents challenges in quantitative and spatial analysis. High-resolution optical imaging techniques show potential in providing detailed 3D spatial, quantitative, and molecular information for better understanding the pancreatic anatomy.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Article
Biochemical Research Methods
Johannes Kuebler, Vincent S. Zoutenbier, Gijs Buist, Joerg Fischer, Arjen Amelink, Johannes F. de Boer
Summary: Optical coherence tomography (OCT) is used for imaging tissue structures, and calibrating intensity values can provide information on the tissue's optical properties. This study explores the feasibility of extracting the focus position from OCT scans using the system's chromatic aberration.
BIOMEDICAL OPTICS EXPRESS
(2023)
Article
Biochemical Research Methods
Gregory N. McKay, Ryan C. Niemeier, Carlos Castro-Gonzalez, Nicholas J. Durr
Summary: The recent application of modern microscopy techniques to human capillary imaging holds great promise for non-invasive alternatives to conventional blood tests. Techniques such as oblique plane microscopy and scattering-contrast oblique plane microscopy have been demonstrated to effectively image blood cells in human capillaries, offering a new avenue for in vivo blood analysis.
BIOMEDICAL OPTICS EXPRESS
(2021)
Review
Medicine, Research & Experimental
Bruce A. Berkowitz, Haohua Qian
Summary: The article reviews high spatial resolution imaging techniques and commercial OCT technologies for measuring mitochondrial respiration in the outer retina, and discusses the importance of changes in subretinal space water content for diagnosing threats to vision and improving treatment success rates.
EXPERIMENTAL BIOLOGY AND MEDICINE
(2021)
Review
Chemistry, Multidisciplinary
Daewoon Seong, Changho Lee, Mansik Jeon, Jeehyun Kim
Summary: In the field of otology, optical coherence tomography (OCT) has played a crucial role in non-invasively obtaining morphological structure of tissues, especially in measuring the entire region of tympanic membrane. Doppler OCT, as a functional extension of OCT, has been applied to combine motion information with structural data of tissue in otology. Over the years, Doppler OCT systems have evolved in various forms to improve the measuring sensitivity of phase difference.
APPLIED SCIENCES-BASEL
(2021)
Review
Ophthalmology
Daniel Lee, Natasha N. Kolomeyer, Reza Razeghinejad, Jonathan S. Myers
Summary: Recent advancements in imaging technology have allowed for real-time assessment of the conventional aqueous outflow pathway, showing promise in expanding our understanding of glaucoma pathogenesis and treatment.
CURRENT OPINION IN OPHTHALMOLOGY
(2021)
Article
Optics
Jianan Fang, Kun Huang, E. Wu, Ming Yan, Heping Zeng
Summary: This article introduces an infrared 3D imaging system capable of detecting three-dimensional structure and reflectivity information. The system operates at single-photon sensitivity and femtosecond timing resolution, enabling imaging under low-light conditions. By nonlinear frequency upconversion and recording with a silicon camera, the presented system achieves high lateral and depth resolutions for 3D reconstruction. Additionally, a numerical denoiser based on spatiotemporal correlation allows the retrieval of object profile and reflectivity even with a detected flux below 0.05 photons/pixel/second. This infrared 3D imager features high detection sensitivity, precise timing resolution, and wide-field operation, offering new possibilities in life and material sciences.
LIGHT-SCIENCE & APPLICATIONS
(2023)
Article
Biotechnology & Applied Microbiology
Di Yang, Weike Wang, Zhuoqun Yuan, Yanmei Liang
Summary: In this study, a high-resolution multi-functional optical coherence tomography (OCT) was used to obtain detailed intra- and extracranial imaging outcomes of adult zebrafish, including pigmentation distribution, tissue-specific information, cranial vascular imaging, and the monitoring of traumatic brain injury (TBI). Additionally, the channels through the zebrafish cranial suture were observed for the first time, which may have a crucial function in maintaining the patency of the cranial sutures. The results demonstrate that the high-resolution multi-functional OCT system can provide a wealth of novel and interpretable biological information for intra- and extracranial studies of adult zebrafish.
BIOENGINEERING-BASEL
(2023)
Article
Acoustics
Efthymios Maneas, Andreas Hauptmann, Erwin J. Alles, Wenfeng Xia, Tom Vercauteren, Sebastien Ourselin, Anna L. David, Simon Arridge, Adrien E. Desjardins
Summary: A framework based on a convolutional neural network (CNN) is proposed to maintain spatial resolution with fewer tracking transmissions and enhance signal quality. Experimental results show that the performance of needle localization can be significantly improved even with an eightfold reduction in tracking transmissions. This framework will greatly improve the performance of ultrasonic tracking, leading to faster image acquisition rates and increased localization accuracy.
IEEE TRANSACTIONS ON ULTRASONICS FERROELECTRICS AND FREQUENCY CONTROL
(2022)
Article
Radiology, Nuclear Medicine & Medical Imaging
Ludovica Brusaferri, Elise C. Emond, Alexandre Bousse, Robert Twyman, Alexander C. Whitehead, David Atkinson, Sebastien Ourselin, Brian F. Hutton, Simon Arridge, Kris Thielemans
Summary: This paper investigates the application of emission-based attenuation correction methods in PET/MR imaging. It addresses the issue of detection efficiency estimation for each energy window and the calibration factor estimation, and compares different reconstruction methods. The results show that there are significant differences in geometric factors between energy windows, and the multiple energy window reconstruction is sensitive to input/model mismatch.
IEEE TRANSACTIONS ON RADIATION AND PLASMA MEDICAL SCIENCES
(2022)
Article
Computer Science, Interdisciplinary Applications
Meghdoot Mozumder, Andreas Hauptmann, Ilkka Nissila, Simon R. Arridge, Tanja Tarvainen
Summary: Diffuse optical tomography (DOT) utilizes near-infrared light to image optical parameters, but faces ill-posedness. Bayesian approach and deep learning can improve image reconstruction. The proposed approach provides accurate and computationally efficient solutions.
IEEE TRANSACTIONS ON MEDICAL IMAGING
(2022)
Article
Acoustics
Arttu Arjas, Erwin J. Alles, Efthymios Maneas, Simon Arridge, Adrien Desjardins, Mikko J. Sillanpaa, Andreas Hauptmann
Summary: This study presents a technique that combines neural network training and Kalman filtering to achieve accurate and robust object localization and quantification in ultrasound imaging using synthetic training data and experimental data. Results show that the proposed method provides reliable and precise positional information in both simulated and experimental data, with the most accurate 3-D localization for elevational distances greater than approximately 1mm.
IEEE TRANSACTIONS ON ULTRASONICS FERROELECTRICS AND FREQUENCY CONTROL
(2022)
Article
Multidisciplinary Sciences
Mathew Van de Pette, Antonio Galvao, Steven J. Millership, Wilson To, Andrew Dimond, Chiara Prodani, Grainne McNamara, Ludovica Bruno, Alessandro Sardini, Zoe Webster, James McGinty, Paul French, Anthony G. Uren, Juan Castillo-Fernandez, Rosalind M. John, Anne C. Ferguson-Smith, Matthias Merkenschlager, Gavin Kelsey, Amanda G. Fisher, William Watkinson
Summary: This study demonstrates that a high-fat diet in pregnant mice can lead to the release of silencing of the Dlk1 gene locus in multiple generations of offspring. The authors found that this occurs through changes in microRNA expression and transcriptional changes in the developing oocytes. These findings highlight how diet can impact the fetal epigenome, affecting the properties of successive generations of offspring through intergenerational or trans-generational mechanisms.
NATURE COMMUNICATIONS
(2022)
Review
Cardiac & Cardiovascular Systems
Tevfik F. Ismail, Wendy Strugnell, Chiara Coletti, Masa Bozic-Iven, Sebastian Weingaertner, Kerstin Hammernik, Teresa Correia, Thomas Kuestner
Summary: Cardiovascular disease is the leading cause of death worldwide, and cardiovascular magnetic resonance has emerged as an important technique for assessing cardiovascular health. However, there are limitations to its widespread use due to the complexity of imaging and analysis methods. This review covers the basics of CMR physics, CVD identification methods, planning and conducting a CMR exam, imaging acceleration and reconstruction techniques, and recent advances in deep learning-based reconstructions and analysis methods.
FRONTIERS IN CARDIOVASCULAR MEDICINE
(2022)
Article
Cardiac & Cardiovascular Systems
Joao Tourais, Cian M. Scannell, Torben Schneider, Ebraham Alskaf, Richard Crawley, Filippo Bosio, Javier Sanchez-Gonzalez, Mariya Doneva, Christophe Schuelke, Jakob Meineke, Jochen Keupp, Jouke Smink, Marcel Breeuwer, Amedeo Chiribiri, Markus Henningsson, Teresa Correia
Summary: This study developed and tested a new cardiac MR imaging technique called FOSTERS for high-resolution imaging of the heart without the need for breath-holding. The technique produced high-quality images and allowed for quantification of myocardial blood flow. Compared to standard breath-hold imaging, FOSTERS provided excellent image quality and comparable blood flow measurements.
FRONTIERS IN CARDIOVASCULAR MEDICINE
(2022)
Article
Computer Science, Artificial Intelligence
Alain Lalande, Zhihao Chen, Thibaut Pommier, Thomas Decourselle, Abdul Qayyum, Michel Salomon, Dominique Ginhac, Youssef Skandarani, Arnaud Boucher, Khawla Brahim, Marleen de Bruijne, Robin Camarasa, Teresa M. Correia, Xue Feng, Kibrom B. Girum, Anja Hennemuth, Markus Huellebrand, Raabid Hussain, Matthias Ivantsits, Jun Ma, Craig Meyer, Rishabh Sharma, Jixi Shi, Nikolaos V. Tsekos, Marta Varela, Xiyue Wang, Sen Yang, Hannu Zhang, Yichi Zhang, Yuncheng Zhou, Xiahai Zhuang, Raphael Couturier, Fabrice Meriaudeau
Summary: This paper presents the results of the EMIDEC challenge, which aims to automatically assess the state of the heart after myocardial infarction (MI). The challenge focuses on distinguishing between non-infarct and pathological exams and automatically calculating the extent of myocardial infarction using deep learning methods. The results show that automatic classification of exams is achievable, and the segmentation of the myocardium is possible, although the segmentation of the diseased area needs improvement.
MEDICAL IMAGE ANALYSIS
(2022)
Article
Mathematics, Applied
Riccardo Barbano, Zeljko Kereta, Andreas Hauptmann, Simon R. Arridge, Bangti Jin
Summary: This research proposes a novel unsupervised knowledge-transfer paradigm for learned reconstruction in medical imaging within a Bayesian framework. The approach learns a reconstruction network in two phases and is capable of delivering predictive uncertainty information over the reconstructed image. Experimental results demonstrate the competitiveness of the approach in low-dose and sparse-view computed tomography, with significant improvements in reconstruction quality both visually and quantitatively.
Article
Biochemical Research Methods
Connor Darling, Samuel P. X. Davis, Sunil Kumar, Paul M. W. French, James McGinty
Summary: This paper presents a single-shot adaptive Optical Projection Tomography (OPT) system for high-speed imaging of dynamic mesoscopic biological samples. The system has the advantages of low cost and no need for sample rotation.
JOURNAL OF BIOPHOTONICS
(2023)
Article
Computer Science, Interdisciplinary Applications
Robert Twyman, Simon Arridge, Zeljko Kereta, Bangti Jin, Ludovica Brusaferri, Sangtae Ahn, Charles W. Stearns, Brian F. Hutton, Irene A. Burger, Fotis Kotasidis, Kris Thielemans
Summary: Penalised PET image reconstruction algorithms can be improved by using a relaxed step size sequence and stochastic variance reduction gradient algorithms (SAGA and SVRG) for faster convergence. Numerical studies show that SAGA and SVRG outperform BSREM in terms of voxel value variations and step size selection. These algorithms can achieve faster convergence to the penalised maximum likelihood solution, especially in low count data.
IEEE TRANSACTIONS ON MEDICAL IMAGING
(2023)
Article
Biology
Hannah J. J. Gleneadie, Beatriz Fernandez-Ruiz, Alessandro Sardini, Mathew Van de Pette, Andrew Dimond, Rab K. K. Prinjha, James McGinty, Paul M. W. French, Hakan Bagci, Matthias Merkenschlager, Amanda G. G. Fisher
Summary: Duchenne muscular dystrophy (DMD) is a genetic disorder caused by mutations in the dystrophin gene (Dmd), leading to progressive muscle weakening. A study using mouse models and myoblasts found that chromatin-modifying drugs can increase the expression of utrophin (Utrn), a protein that can compensate for Dmd deficiency. Inhibitors of PRC2 and ERK1/2 were identified to enhance Utrn expression, offering potential therapeutic strategies for DMD.
COMMUNICATIONS BIOLOGY
(2023)
Article
Acoustics
Antonio Stanziola, Simon Arridge, Ben T. Cox, Bradley E. Treeby
Summary: A new method called the learned Born series (LBS) is introduced for solving the wave equation, where the components of the LBS are determined through training. The LBS is found to be more accurate than the convergent Born series for the same number of iterations, especially in the presence of high contrast scatterers, while maintaining a similar computational complexity. It is capable of generating a reasonable prediction of the global pressure field with a small number of iterations, and the errors decrease with the number of learned iterations.
JASA EXPRESS LETTERS
(2023)
Article
Microscopy
J. Lightley, S. Kumar, M. Q. Lim, E. Garcia, F. Goerlitz, Y. Alexandrov, T. Parrado, C. Hollick, E. Steele, K. Rossmann, J. Graham, J. Broichhagen, I. A. Mcneish, C. A. Roufosse, M. A. A. Neil, C. Dunsby, P. M. W. French
Summary: 'openFrame' is a modular, low-cost, open-hardware microscopy platform that can be configured or adapted to most light microscopy techniques and allows for rapid prototyping and automation.
JOURNAL OF MICROSCOPY
(2023)