Article
Biochemical Research Methods
Yuanyuan Li, Jun Wu, Donghuan Lu, Chao Xu, Yefeng Zheng, Hanchuan Peng, Lei Qu
Summary: Recent whole-brain mapping projects are collecting larger sets of high-resolution brain images using various techniques. Reliable cross-modal registration tools are needed for data mining and analysis. mBrainAligner-Web is a user-friendly web server that allows configuration and execution of mBrainAligner locally or remotely across platforms.
Article
Biochemical Research Methods
L. Silvestri, M. C. Mullenbroich, I. Costantini, A. P. Di Giovanna, G. Mazzamuto, A. Franceschini, D. Kutra, A. Kreshuk, C. Checcucci, L. O. Toresano, P. Frasconi, L. Sacconi, F. S. Pavone
Summary: RAPID is a real-time autofocus method for widefield microscopy that removes image degradation in large, cleared samples for enhanced quantitative analyses. It enables high-resolution imaging of macroscopic biological samples and allows for 3D spatial clustering analysis of neurons and morphological analysis of microglia. Beyond light-sheet microscopy, RAPID also maintains high image quality in various settings, making it suitable for traditional automated microscopy tasks and quantitative analysis of large biological specimens.
Article
Multidisciplinary Sciences
Felix A. Kyere, Ian Curtin, Oleh Krupa, Carolyn M. McCormick, Mustafa Dere, Sarah Khan, Minjeong Kim, Tzu-Wen Winnie Wang, Qiuhong He, Guorong Wu, Yen-Yu Ian Shih, Jason L. Stein
Summary: Tissue clearing combined with light-sheet microscopy enables cellular-resolution imaging of intact brain structure, allowing quantitative analysis of structural changes caused by genetic or environmental perturbations. The use of light-sheet microscopy for imaging cleared brains increases acquisition speed, but current computational tools are limited in quantifying sparse cell populations.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2022)
Article
Computer Science, Artificial Intelligence
Xinrui Song, Hanqing Chao, Xuanang Xu, Hengtao Guo, Sheng Xu, Baris Turkbey, Bradford J. Wood, Thomas Sanford, Ge Wang, Pingkun Yan
Summary: This paper introduces a novel cross-modal attention mechanism for medical image registration, along with a contrastive learning-based pre-training method to improve network performance.
MEDICAL IMAGE ANALYSIS
(2022)
Article
Multidisciplinary Sciences
Songwei Wang, Yuhang Wang, Ke Niu, Qian Li, Xiaoping Rao, Hui Zhao, Liwei Chen, Li Shi
Summary: This study introduces a novel method based on the JEMI network to solve the issue of regional localization in brain science research. By converting the brain slice and ARA into a segmentation map with unified modality, the method effectively overcomes the influence of non-unified modal images and achieves accurate and rapid localization of the brain slice.
Editorial Material
Biology
Hovy Ho-Wai Wong, Christina You Chien Chou, Alanna Jean Watt, Per Jesper Sjoestroem
Summary: This statement points out that inhibitory circuit motifs in the mouse brain and the human brain are remarkably similar.
Article
Multidisciplinary Sciences
Chandler D. Gatenbee, Ann-Marie Baker, Sandhya Prabhakaran, Ottilie Swinyard, Robbert J. C. Slebos, Gunjan Mandal, Eoghan Mulholland, Noemi Andor, Andriy Marusyk, Simon Leedham, Jose R. Conejo-Garcia, Christine H. Chung, Mark Robertson-Tessi, Trevor A. Graham, Alexander R. A. Anderson
Summary: Interest in spatial omics is growing, but generating highly multiplexed images is challenging due to various factors. A new software called VALIS has been developed to address these challenges by aligning whole slide images (WSI) and generating high-quality, spatially aligned datasets. VALIS provides state-of-the-art accuracy in WSI registration and 3D reconstruction, making it a valuable tool for spatial studies of tumor ecology.
NATURE COMMUNICATIONS
(2023)
Article
Biology
Antoine Beauchamp, Yohan Yee, Ben C. Darwin, Armin Raznahan, Rogier B. Mars, Jason P. Lerch
Summary: Researchers use a common reference space approach to evaluate the similarity between mouse and human brain, finding that mouse-human homologous genes can capture general patterns of neuroanatomical organization. By using a supervised machine learning approach, the resolution of cross-species correspondences can be improved.
Article
Immunology
Fares Bassil, Emily S. Meymand, Hannah J. Brown, Hong Xu, Timothy O. Cox, Shankar Pattabhiraman, Chantal M. Maghames, Qihui Wu, Bin Zhang, John Q. Trojanowski, Virginia M. -Y. Lee
Summary: The neuropathological hallmarks of Parkinson's disease (PD) and Alzheimer's disease (AD), alpha-synuclein (alpha-syn) and tau aggregates, may interact in patients with these diseases, with alpha-syn playing an important modulatory role in the burden and spreading of tau pathology.
JOURNAL OF EXPERIMENTAL MEDICINE
(2021)
Article
Computer Science, Information Systems
Chengyuan Zhang, Jiayu Song, Xiaofeng Zhu, Lei Zhu, Shichao Zhang
Summary: The Hybrid Cross-Modal Similarity Learning model (HCMSL) proposed in this article effectively addresses the similarity measurement issue in cross-modal retrieval by capturing semantic information and establishing a common subspace between different modalities. Comprehensive experiments demonstrate significant improvements over existing techniques on real datasets.
ACM TRANSACTIONS ON MULTIMEDIA COMPUTING COMMUNICATIONS AND APPLICATIONS
(2021)
Article
Computer Science, Information Systems
Anusha Achuthan, Mandava Rajeswari
Summary: Segmentation of subcortical structures like the hippocampus in brain MR images is challenging due to weak or unclear boundary definitions, especially at the head and tail. An automated segmentation approach showed promising results with an average Dice Similarity Coefficient of 0.8050 on public datasets, comparable to other state-of-the-art approaches.
JOURNAL OF KING SAUD UNIVERSITY-COMPUTER AND INFORMATION SCIENCES
(2021)
News Item
Multidisciplinary Sciences
Saima May Sidik
Summary: A platelet factor is added to the list of blood components that may have anti-aging effects.
Article
Computer Science, Information Systems
Qiubin Lin, Wenming Cao, Zhiquan He, Zhihai He
Summary: The rapid development of deep learning has led to significant progress in cross-modal retrieval and the recent attention towards cross-modal hashing. The existing semantic heterogeneity gap between different modalities presents a challenging problem. To address this, we propose the MDCH approach, which introduces semantic mask information and alternately trains intra-modal and inter-modal networks to improve hash code effectiveness.
IEEE TRANSACTIONS ON MULTIMEDIA
(2021)
Article
Computer Science, Artificial Intelligence
Alan Q. Wang, Evan M. Yu, Adrian V. Dalca, Mert R. Sabuncu
Summary: KeyMorph is a deep learning-based image registration framework that enhances robustness and interpretability by automatically detecting corresponding keypoints, incorporating symmetries, and handling image translations. This framework shows excellent performance in solving the registration problem of multi-modal brain MRI scans.
MEDICAL IMAGE ANALYSIS
(2023)
Article
Multidisciplinary Sciences
Ching-Wei Wang, Yu-Ching Lee, Muhammad-Adil Khalil, Kuan-Yu Lin, Cheng-Ping Yu, Huang-Chun Lien
Summary: Joint analysis of multiple protein expressions and tissue morphology patterns is crucial for disease diagnosis and drug development. However, aligning enormous gigapixel whole slide images (WSIs) with different staining is challenging. This study proposes an image registration framework that achieves accurate and real-time cross-staining alignment of gigapixel WSIs, showing great potential in assisting medical doctors in cancer diagnosis and staging.
SCIENTIFIC REPORTS
(2022)
Article
Biology
Chuan Huang, Yu Wang, Peng Chen, Qing-Hong Shan, Hao Wang, Lu-Feng Ding, Guo-Qiang Bi, Jiang-Ning Zhou
Summary: This study used a rabies-virus system to map the single-cell input onto corticotropin-releasing factor (CRF) neurons in the central amygdala (CeA). The inputs were found to be located in 44 nested subregions, with most of them being top-down convergent inputs from the cortex, especially in layer 4 of the somatosensory cortex, and relaying information from the thalamus. The bottom-up divergent inputs had a higher expression of glutamate decarboxylase. The study also revealed the en passant structures of single input neurons through in-situ reconstruction. These findings provide valuable insights into the circuit mechanisms of CeA-CRF neurons.
COMMUNICATIONS BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Zhaohuan Huang, Ling Liu, Jian Zhang, Kristie Conde, Jay Phansalkar, Zhongzhong Li, Lei Yao, Zihui Xu, Wei Wang, Jiangning Zhou, Guoqiang Bi, Feng Wu, Randy J. Seeley, Michael M. Scott, Cheng Zhan, Zhiping P. Pang, Ji Liu
Summary: This study identified a population of glucose-sensing GLP-1 receptor neurons in the dorsomedial hypothalamic nucleus, which can decrease blood glucose levels through communication with the pancreas. The mechanism by which this central GLP-1 signal controls glucose levels was also elucidated.
Article
Neurosciences
Qiao-Qiong Liu, Yu-Xiao Cheng, Qi Jing, Ke-Ming Zhang, Lu-Feng Ding, Xiao-Wei Fan, Chun-Hui Jia, Fang Xu, Guo-Qiang Bi, Pak-Ming Lau
Summary: This study employed a dual-viral injection strategy to label cortical pyramidal neurons targeting the pedunculopontine nucleus (PPN) in mice. By using a high-speed volumetric imaging technique, the researchers visualized the brain-wide axonal projections of these neurons from various cortical areas and identified unique collateralization patterns to different subcortical areas. The findings provide potential anatomical mechanisms for the coordination between the PPN and other subcortical areas in performing different physiological functions.
Article
Neurosciences
Xiao-Wei Li, Yi Ren, Dong-Qing Shi, Lei Qi, Fang Xu, Yanyang Xiao, Pak-Ming Lau, Guo-Qiang Bi
Summary: Acetylcholine (ACh) affects neural circuit dynamics by inhibiting excitatory synaptic transmission and enhancing neuronal excitability through muscarinic signaling pathways. It suppresses evoked reverberation at low to moderate doses, while high doses result in longer duration of reverberation and increased spontaneous activity. These effects are mediated by muscarinic, but not nicotinic receptors, and can be simulated through changes in excitatory postsynaptic currents (EPSCs) and the excitability of single cells.
NEUROSCIENCE BULLETIN
(2023)
Article
Cell Biology
Gaowei Chen, Shishi Lai, Guo Bao, Jincan Ke, Xiaogao Meng, Shanshan Lu, Xiaocong Wu, Hua Xu, Fengyi Wu, Yu Xu, Fang Xu, Guo-Qian Bi, Guangdun Peng, Kuikui Zhou, Yingjie Zhu
Summary: The nucleus accumbens (NAc) plays a crucial role in motivation and reward processing. Recent research suggests that different subnuclei of the NAc have distinct contributions to reward-related behaviors. However, how individual NAc neurons encode reward remains unclear.
Letter
Neurosciences
Dong-Qing Shi, Fang Xu, Guo-Qiang Bi, Pak-Ming Lau
NEUROSCIENCE BULLETIN
(2023)
Article
Neurosciences
Ke-Ming Zhang, Yan Shen, Chun-Hui Jia, Hao Wang, Guo-Qiang Bi, Pak-Ming Lau
Summary: Cooperation is a vital social behavior for survival, and a new paradigm was developed to train and test cooperative behavior in mice. The study found extensive social contact and waiting behavior, which were positively correlated with the success of cooperation. Using c-Fos immunostaining and high-speed volumetric imaging, the researchers identified increased neuronal activity in cortical areas during cooperation, providing insights into the underlying neural circuitry mechanisms.
Article
Multidisciplinary Sciences
Xiaofeng Han, Shuxia Guo, Nan Ji, Tian Li, Jian Liu, Xiangqiao Ye, Yi Wang, Zhixi Yun, Feng Xiong, Jing Rong, Di Liu, Hui Ma, Yujin Wang, Yue Huang, Peng Zhang, Wenhao Wu, Liya Ding, Michael Hawrylycz, Ed Lein, Giorgio A. Ascoli, Wei Xie, Lijuan Liu, Liwei Zhang, Hanchuan Peng
Summary: In this study, a unique approach was proposed to collect three-dimensional images of brain neurons by injecting dyes into patients' brain tissues. The research found that human neurons are more diverse across brain regions than by subject age or gender. Furthermore, the strong stereotypy within brain region cohorts allows for the generation of a statistical tensor field of neuron morphology to characterize the anatomical modularity of a human brain.
Article
Neurosciences
Wantong Shi, Man Xue, Fengyi Wu, Kexin Fan, Qi-Yu Chen, Fang Xu, Xu-Hui Li, Guo-Qiang Bi, Jing-Shan Lu, Min Zhuo
Summary: This study examined the axonal outputs of the anterior cingulate cortex (ACC) in the whole brain of adult male mice. The ACC primarily projected ipsilaterally to several regions such as the caudate putamen, ventral thalamic nucleus, zona incerta, periaqueductal gray, superior colliculus, interpolar spinal trigeminal nucleus, and dorsal medullary reticular nucleus. The ACC also projected to contralateral brain regions. These findings provide a whole-brain mapping of the ACC projections in adult male mice and are important for future studies on ACC-related brain diseases.
Article
Neurosciences
Man Xue, Wan-Tong Shi, Si-Bo Zhou, Ya-Nan Li, Feng-Yi Wu, Qi-Yu Chen, Ren-Hao Liu, Zhao-Xiang Zhou, Yu-Xiang Zhang, Yu-Xin Chen, Fang Xu, Guo-Qiang Bi, Xu-Hui Li, Jing-Shan Lu, Min Zhuo
Summary: The anterior cingulate cortex (ACC) plays important roles in pain perception and emotion, with the thalamocortical pathway being the major sensory input. Adult mice, especially genetically modified mice, provide important mechanisms for cortical plasticity and modulation in the ACC. Research found that cortical neurons in the ACC received direct projections from different sub-nuclei in the thalamus.