Article
Neurosciences
Weihao Sheng, Xueyang Zhao, Xinrui Huang, Yang Yang
Summary: The study developed an analysis software called ORCA, which enables real-time analysis of neuronal imaging data including image registration, neuron segmentation, and activity extraction. It also efficiently tracks neurons across multiple sessions, providing a solution for fast imaging data analysis and all-optical closed-loop control of neuronal activity.
FRONTIERS IN CELLULAR NEUROSCIENCE
(2022)
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
Engineering, Biomedical
Zhe Chen, Garrett J. Blair, Chengdi Cao, Jim Zhou, Daniel Aharoni, Peyman Golshani, Hugh T. Blair, Jason Cong
Summary: Miniaturized calcium imaging is a neural recording technique used for monitoring neural activity. An FPGA-based real-time calcium image processing pipeline has been proposed for closed-loop feedback applications, allowing real-time decoding with sub-ms processing latency.
IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITS AND SYSTEMS
(2023)
Article
Multidisciplinary Sciences
Aurelio Cortese, Saori C. Tanaka, Kaoru Amano, Ai Koizumi, Hakwan Lau, Yuka Sasaki, Kazuhisa Shibata, Vincent Taschereau-Dumouchel, Takeo Watanabe, Mitsuo Kawato
Summary: Decoded neurofeedback (DecNef) combines fMRI with machine learning to potentially benefit clinical applications. By releasing datasets from studies, researchers can analyze brain dynamics and modulation mechanisms.
Article
Engineering, Biomedical
Mang Feng, Xu Ji, Ran Zhang, Kevin Treb, Aaron M. Dingle, Ke Li
Summary: This study presents an experimental method for correcting concentric artifacts in PCD-CT images by using pixel-specific polynomial functions to address spectral inconsistency. Experimental evaluation showed that this method effectively reduces low-frequency concentric artifacts in PCD-CT images.
PHYSICS IN MEDICINE AND BIOLOGY
(2021)
Article
Computer Science, Information Systems
Mehmet Sarigul
Summary: Shakes and jitters in video recordings can be eliminated through digital video stabilization using smart algorithms. This process involves camera motion estimation, motion correction, and stable video synthesis. There are different methods in the literature that perform these steps in various ways. Recent advancements in deep learning have introduced learning-based approaches to video stabilization. This paper provides a detailed explanation of video stabilization methods by analyzing and comparing the approaches used from the past to the present.
MULTIMEDIA TOOLS AND APPLICATIONS
(2023)
Article
Computer Science, Information Systems
Jian Gong, Kangjian He, Lisiqi Xie, Dan Xu, Tao Yang
Summary: This paper introduces a novel local quality based curved section encoding strategy for single projection image sequence matching tasks encountered in medical practice. Experimental results demonstrate that this method has good registration performance on CT/CBCT datasets.
Article
Radiology, Nuclear Medicine & Medical Imaging
Brendan T. Crabb, Forrest Hamrick, Tyler Richards, Preston Eiswirth, Frederic Noo, Albert Hsiao, Gabriel C. Fine
Summary: The utility and generalizability of deep learning subtraction angiography (DLSA) for generating synthetic digital subtraction angiography (DSA) images without misalignment artifacts were investigated. A deep neural network pix2pix was trained to produce synthetic DSA images from native digital angiograms. The proposed approach was found to generate synthetic DSA images with fewer background artifacts without a significant difference in foreground vascular detail, and transfer learning significantly improved the quality of generated images. DLSA reliably generates synthetic angiograms without misalignment artifacts and can be applied to novel vasculature.
JOURNAL OF VASCULAR AND INTERVENTIONAL RADIOLOGY
(2023)
Article
Computer Science, Interdisciplinary Applications
Rafael C. Schick, Thomas Koehler, Wolfgang Noichl, Fabio De Marco, Konstantin Willer, Theresa Urban, Manuela Frank, Thomas Pralow, Ingo Maack, Sven Prevrhal, Bernd Lundt, Alexander Fingerle, Daniela Pfeiffer, Julia Herzen, Franz Pfeiffer
Summary: Dark-field radiography is a promising imaging technique for early diagnosis of lung diseases, but prolonged image acquisition time can lead to motion artifacts. A motion artifact reduction algorithm was developed and successfully evaluated in simulated chest phantom and in vivo human data, significantly improving the image quality of dark-field chest X-ray radiographs by reducing motion artifacts.
IEEE TRANSACTIONS ON MEDICAL IMAGING
(2022)
Article
Computer Science, Artificial Intelligence
Veronica Corona, Angelica Aviles-Rivero, Noemie Debroux, Carole Le Guyader, Carola-Bibiane Schonlieb
Summary: The study introduces a variational multi-task framework that combines reconstruction, registration, and super-resolution tasks in MRI to achieve high-quality, motion-free image reconstructions with fine details and improved texture compared to state-of-the-art methods.
MEDICAL IMAGE ANALYSIS
(2021)
Article
Mathematical & Computational Biology
Weiyi Liu, Junxia Pan, Yuanxu Xu, Meng Wang, Hongbo Jia, Kuan Zhang, Xiaowei Chen, Xingyi Li, Xiang Liao
Summary: This study proposes a fast and accurate motion correction method based on image density features for two-photon Ca2+ imaging data. The method robustly estimates and clusters density features, and takes advantage of temporal correlation in the imaging data to quickly and accurately correct motion artifacts. The research shows that this method has high computational efficiency and performs well in motion correction for imaging data at different scales.
FRONTIERS IN NEUROINFORMATICS
(2022)
Article
Radiology, Nuclear Medicine & Medical Imaging
Mehrgan Shahryari, Tom Meyer, Carsten Warmuth, Helge Herthum, Gergely Bertalan, Heiko Tzschatzsch, Lisa Stencel, Steffen Lukas, Ledia Lilaj, Jurgen Braun, Ingolf Sack
Summary: This study analyzed the effect of different breathing strategies on multifrequency magnetic resonance elastography of abdominal organs. The results showed that free-breathing MRE resulted in larger organ displacements but did not affect shear wave speed, and image registration improved the quality of examinations.
MAGNETIC RESONANCE IN MEDICINE
(2021)
Article
Radiology, Nuclear Medicine & Medical Imaging
Markus M. Obmann, Yuxin Sun, Chansik An, Michael A. Ohliger, Zhen J. Wang, Benjamin M. Yeh
Summary: This study evaluated the influence of different DECT scanners and enteric contrast agents on the severity of bowel peristalsis artifact in vitro. The results showed that peristalsis artifact severity varied among different DECT scanners, with experimental dark bowel contrast material reducing peristalsis artifact compared to other contrast agents.
AMERICAN JOURNAL OF ROENTGENOLOGY
(2022)
Article
Automation & Control Systems
Yuyu Guo, Lei Bi, Dongming Wei, Liyun Chen, Zhengbin Zhu, Dagan Feng, Ruiyan Zhang, Qian Wang, Jinman Kim
Summary: In this study, we propose a dense-sparse-dense (DSD) motion estimation framework that utilizes unsupervised 3D landmark detection network and motion reconstruction network to extract sparse landmarks and construct motion field in two stages. The method improves the accuracy of motion estimation and preserves anatomical topology.
IEEE TRANSACTIONS ON CYBERNETICS
(2023)
Article
Radiology, Nuclear Medicine & Medical Imaging
I. A. Tsalafoutas, V Tsapaki, I Triantopoulou
Summary: The study investigates the impact of X-ray preset acquisition protocol settings on fluoroscopy image quality and radiation exposure. Results show that protocol selection affects radiation exposure significantly by a factor of about 3. Evaluation of image quality revealed differences in characteristics between images produced by different acquisition protocols, with the visual IQ evaluation method being time-consuming and cumbersome.
EUROPEAN JOURNAL OF RADIOLOGY
(2021)
Article
Neurosciences
An Wu, Bin Yu, Takaki Komiyama
CURRENT OPINION IN NEUROBIOLOGY
(2020)
Article
Neurosciences
Zhengyu Ma, Haixin Liu, Takaki Komiyama, Ralf Wessel
JOURNAL OF NEUROPHYSIOLOGY
(2020)
Article
Chemistry, Multidisciplinary
Mark Bathe, Rigoberto Hernandez, Takaki Komiyama, Raghu Machiraju, Sanghamitra Neogi
Summary: Conventional materials are facing limitations in computation, sensing, and data storage, while the human brain excels in integrated sensing, computation, and data storage with minimal energy consumption. The proposed autonomous computing materials aim to mimic the brain's capabilities for integrated functions, offering transformative opportunities for distributed, multimodal sensing, computation, and data storage.
Article
Neurosciences
Chi Ren, Takaki Komiyama
Summary: Wide-field calcium imaging, combined with genetically encoded calcium indicators, allows for real-time capture of cortex-wide dynamics in behaving animals and has revealed unprecedented scale of cortical dynamics during various cognitive processes.
JOURNAL OF NEUROSCIENCE
(2021)
Article
Neurosciences
Xin Liu, Chi Ren, Yichen Lu, Yixiu Liu, Jeong-Hoon Kim, Stefan Leutgeb, Takaki Komiyama, Duygu Kuzum
Summary: The authors introduced a flexible, insertable, and transparent microelectrode array, Neuro-FITM, for multimodal recordings of cortical and hippocampal activity patterns. They demonstrated that diverse cortical activity patterns accompanied hippocampal sharp-wave ripples, with cortical activation often preceding the ripples. This suggests a selective and diverse interaction between hippocampal and large-scale cortical activity during sharp-wave ripples, underlying various cognitive functions.
NATURE NEUROSCIENCE
(2021)
Article
Neurosciences
Eun Jung Hwang, Jeffrey E. Dahlen, Madan Mukundan, Takaki Komiyama
Summary: It has been found that the dependence on the motor cortex during long-term learning is not fixed, but can dynamically change. Movements that achieve higher consistency are less dependent on the motor cortex, and superior motor performance can affect neural circuit reorganization.
JOURNAL OF NEUROSCIENCE
(2021)
Article
Engineering, Biomedical
Xin Liu, Chi Ren, Zhisheng Huang, Madison Wilson, Jeong-Hoon Kim, Yichen Lu, Mehrdad Ramezani, Takaki Komiyama, Duygu Kuzum
Summary: The study demonstrates that locally recorded surface potentials contain rich information about large-scale neural activities, which can be decoded to recover neural activity across individual cortical regions. Including all frequency bands in the decoding model results in the highest decoding performance, and incorporating more recording channels improves the decoding performance even further. This cross-modality inference approach has the potential to reconstruct cortex-wide brain activity in a non-invasive manner and facilitate imaging neural activity in freely moving animals without the need for head-fixed microscopy configurations.
JOURNAL OF NEURAL ENGINEERING
(2021)
Article
Neurosciences
Ryoma Hattori, Takaki Komiyama
Summary: Task-related information is coded with different persistency across the brain. The coding persistency of action history and value in mice varies across areas, learning phases, and task context, with the highest persistency observed in the retrosplenial cortex of expert mice. Persistent coding enables robust signal coding and distribution in neuronal networks.
Article
Neurosciences
Saber Meamardoost, Mahasweta Bhattacharya, Eun Jung Hwang, Takaki Komiyama, Claudia Mewes, Linbing Wang, Ying Zhang, Rudiyanto Gunawan
Summary: The study developed a MATLAB package called FARCI for inferring neuronal connectomes from high-dimensional two-photon Calcium fluorescence data, using partial correlations as a measure of functional association strength between neuron pairs. Testing on simulated datasets demonstrated that FARCI provides accurate connectomes and is robust to network sizes, missing neurons, and noise levels. Compared to other algorithms, FARCI produces more accurate networks, with better computational speed and scalability.
Article
Neurosciences
Nathan G. Hedrick, Zhongmin Lu, Eric Bushong, Surbhi Singhi, Peter Nguyen, Yessenia Magana, Sayyed Jilani, Byung Kook Lim, Mark Ellisman, Takaki Komiyama
Summary: Learning induces the formation of new dendritic spines, which bind new presynaptic inputs into preexisting clusters, generating locally coherent inputs representing learned behaviors. Successful connections are selected based on co-activity with nearby task-related spines, ensuring the functional clustering of new spines. Furthermore, a majority of new spines synapse with previously unrepresented axons, suggesting the binding of new information into functional synaptic clusters.
NATURE NEUROSCIENCE
(2022)
Article
Neurosciences
Chi Ren, Kailong Peng, Ruize Yang, Weikang Liu, Chang Liu, Takaki Komiyama
Summary: This study found that different subtypes of inhibitory neurons (INs) in the cortex of mice learning a task are globally modulated throughout the cortex, with initial learning involving varying levels of activation of VIP-INs and SOM-INs. Furthermore, manipulation of the cholinergic system can affect the activity of cortical IN subtypes and subsequently impact motor learning.
Article
Engineering, Biomedical
Fangyu Liu, Saber Meamardoost, Rudiyanto Gunawan, Takaki Komiyama, Claudia Mewes, Ying Zhang, EunJung Hwang, Linbing Wang
Summary: In this study, deep learning was applied to neural decoding, and the performance of different decoding schemes was evaluated. The results showed that deep learning networks outperformed traditional machine learning algorithms in some decoding schemes, indicating the potential of deep learning for behavior decoding.
JOURNAL OF NEURAL ENGINEERING
(2022)
Article
Biochemical Research Methods
Ryoma Hattori, Takaki Komiyama
Summary: PatchWarp is a registration algorithm developed to correct slow image distortion in calcium imaging data. It combines rigid and non-rigid registrations to robustly correct non-uniform distortions and provides a fully automated method for registering images from different imaging sessions. PatchWarp improves the quality of neural activity analyses and is useful for correcting image distortions in a wide range of disciplines.
CELL REPORTS METHODS
(2022)
Article
Biochemical Research Methods
Ryoma Hattori, Takaki Komiyama
Summary: This article describes a protocol for longitudinal in vivo two-photon calcium imaging using an ultra-large cranial window in head-fixed mice. The protocol allows tracking neural activity from different cortical areas at cellular resolution to understand cortical computations during behavioral tasks.
Article
Biochemical Research Methods
Chi Ren, Takaki Komiyama
Summary: Characterizing cortex-wide neural activity through wide-field calcium imaging in awake, head-fixed mice allows for capturing large-scale neural activity with sufficient signal-to-noise ratio and spatiotemporal resolution. The use of genetically encoded calcium indicators enables longitudinal imaging and cell-type specificity. A processing pipeline for imaging data is also described.
