Challenges of Processing and Analyzing Big Data in Mesoscopic Whole-brain Imaging

Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China MOE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan 430074, China HUST-Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou 215125, China

[1]  Fernando Amat,et al.  Efficient processing and analysis of large-scale light-sheet microscopy data , 2015, Nature Protocols.

[2]  Henry Markram,et al.  A Cell Atlas for the Mouse Brain , 2018, Front. Neuroinform..

[3]  Adam R Ferguson,et al.  Big data from small data: data-sharing in the 'long tail' of neuroscience , 2014, Nature Neuroscience.

[4]  Arnon Rosenthal,et al.  Methodological Review: Cloud computing: A new business paradigm for biomedical information sharing , 2010 .

[5]  Qingming Luo,et al.  A Robust Image Registration Interface for Large Volume Brain Atlas , 2018, Scientific Reports.

[6]  David Baker,et al.  Algorithm discovery by protein folding game players , 2011, Proceedings of the National Academy of Sciences.

[7]  H. Markram The Blue Brain Project , 2006, Nature Reviews Neuroscience.

[8]  G. Allan Johnson,et al.  Digital Atlasing and Standardization in the Mouse Brain , 2011, PLoS Comput. Biol..

[9]  Ian R. Wickersham,et al.  The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas , 2017, Neuron.

[10]  Hanchuan Peng,et al.  Reconstructing the brain: from image stacks to neuron synthesis , 2016, Brain Informatics.

[11]  Jan Flusser,et al.  Image registration methods: a survey , 2003, Image Vis. Comput..

[12]  Zoran Popović,et al.  Power to the People: Addressing Big Data Challenges in Neuroscience by Creating a New Cadre of Citizen Neuroscientists , 2016, Neuron.

[13]  Hongkui Zeng,et al.  Neuroinformatics of the Allen Mouse Brain Connectivity Atlas. , 2015, Methods.

[14]  Gerald M. Rubin,et al.  Cortical column and whole-brain imaging with molecular contrast and nanoscale resolution , 2019, Science.

[15]  Gilson A. Giraldi,et al.  Distributed Visualization Using VTK in Grid Environments , 2007, Seventh IEEE International Symposium on Cluster Computing and the Grid (CCGrid '07).

[16]  Valerio Pascucci,et al.  A Virtual Reality Visualization Tool for Neuron Tracing , 2018, IEEE Transactions on Visualization and Computer Graphics.

[17]  Won-Ki Jeong,et al.  Whole-brain serial-section electron microscopy in larval zebrafish , 2017, Nature.

[18]  Hongkui Zeng,et al.  Mesoscale connectomics , 2018, Current Opinion in Neurobiology.

[19]  Jeremy D. Schmahmann,et al.  A Proposal for a Coordinated Effort for the Determination of Brainwide Neuroanatomical Connectivity in Model Organisms at a Mesoscopic Scale , 2009, PLoS Comput. Biol..

[20]  Sara Reardon,et al.  A giant neuron found wrapped around entire mouse brain , 2017, Nature.

[21]  Wei Ge,et al.  The Sunway TaihuLight supercomputer: system and applications , 2016, Science China Information Sciences.

[22]  R. Grossman,et al.  A vision for a biomedical cloud , 2012, Journal of internal medicine.

[23]  Yves Frégnac,et al.  Big data and the industrialization of neuroscience: A safe roadmap for understanding the brain? , 2017, Science.

[24]  M W Marcellin,et al.  Three-dimensional image compression with integer wavelet transforms. , 2000, Applied optics.

[25]  P. Osten,et al.  Mapping brain circuitry with a light microscope , 2013, Nature Methods.

[26]  T. Insel,et al.  The NIH BRAIN Initiative , 2013, Science.

[27]  Ruchi Parekh,et al.  Neuronal Morphology Goes Digital: A Research Hub for Cellular and System Neuroscience , 2013, Neuron.

[28]  Cyriel M A Pennartz,et al.  Data integration through brain atlasing: Human Brain Project tools and strategies , 2018, European Psychiatry.

[29]  Jane Qiu Research and development of artificial intelligence in China , 2016 .

[30]  QingMing Luo Brainsmatics—bridging the brain science and brain-inspired artificial intelligence , 2017 .

[31]  Arie E. Kaufman,et al.  Visualization of Neuronal Structures in Wide-Field Microscopy Brain Images , 2019, IEEE Transactions on Visualization and Computer Graphics.

[32]  Jing Yuan,et al.  TDat: An Efficient Platform for Processing Petabyte-Scale Whole-Brain Volumetric Images , 2017, Front. Neural Circuits.

[33]  S. Herculano‐Houzel The Human Brain in Numbers: A Linearly Scaled-up Primate Brain , 2009, Front. Hum. Neurosci..

[34]  J. D. Macklis,et al.  Multipotent neural precursors can differentiate toward replacement of neurons undergoing targeted apoptotic degeneration in adult mouse neocortex. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[35]  Sten Grillner,et al.  Global Neuroinformatics: The International Neuroinformatics Coordinating Facility , 2007, The Journal of Neuroscience.

[36]  Wojciech Matusik,et al.  3D TV: a scalable system for real-time acquisition, transmission, and autostereoscopic display of dynamic scenes , 2004, ACM Trans. Graph..

[37]  Ioannis A. Kakadiaris,et al.  Landmark-Driven, Atlas-Based Segmentation of Mouse Brain Tissue Images Containing Gene Expression Data , 2004, MICCAI.

[38]  Tobias Pietzsch,et al.  BigDataViewer: visualization and processing for large image data sets , 2015, Nature Methods.

[39]  Alex Gomez-Marin Focus on big data , 2014, Nature Neuroscience.

[40]  Shaoqun Zeng,et al.  Cell-type-specific and projection-specific brain-wide reconstruction of single neurons , 2018, Nature Methods.

[41]  Hongkui Zeng,et al.  Generation of a whole-brain atlas for the cholinergic system and mesoscopic projectome analysis of basal forebrain cholinergic neurons , 2017, Proceedings of the National Academy of Sciences.

[42]  Alan C. Evans,et al.  BigBrain: An Ultrahigh-Resolution 3D Human Brain Model , 2013, Science.

[43]  Miao He,et al.  Brain-wide Maps Reveal Stereotyped Cell-Type-Based Cortical Architecture and Subcortical Sexual Dimorphism , 2017, Cell.

[44]  K. Venkataraju,et al.  Oblique light-sheet tomography: fast and high resolution volumetric imaging of mouse brains , 2017, bioRxiv.

[45]  Q. Luo,et al.  A Quantitative Analysis of the Distribution of CRH Neurons in Whole Mouse Brain , 2017, Front. Neuroanat..

[46]  Christof Koch,et al.  Worldwide initiatives to advance brain research , 2016, Nature Neuroscience.

[47]  W. Denk,et al.  The Big and the Small: Challenges of Imaging the Brain’s Circuits , 2011, Science.

[48]  Jayaram Chandrashekar,et al.  Long distance projections of cortical pyramidal neurons , 2018, Journal of neuroscience research.

[49]  L. Luo,et al.  It takes the world to understand the brain , 2015, Science.

[50]  张斌,et al.  Micro-Optical Sectioning Tomography to Obtain a High-Resolution Atlas of the Mouse Brain , 2010 .

[51]  Javier DeFelipe Neuroanatomy and Global Neuroscience , 2017, Neuron.

[52]  David Cyranoski Beijing launches pioneering brain-science centre , 2018, Nature.

[53]  Karel Svoboda,et al.  A platform for brain-wide imaging and reconstruction of individual neurons , 2016, eLife.

[54]  Jeremy Freeman Open source tools for large-scale neuroscience , 2015, Current Opinion in Neurobiology.

[55]  Partha P. Mitra,et al.  The Circuit Architecture of Whole Brains at the Mesoscopic Scale , 2014, Neuron.

[56]  G. Allan Johnson,et al.  Waxholm Space: An image-based reference for coordinating mouse brain research , 2010, NeuroImage.

[57]  H. Gong,et al.  A platform for stereological quantitative analysis of the brain-wide distribution of type-specific neurons , 2017, Scientific Reports.

[58]  Krzysztof J. Gorgolewski,et al.  Making big data open: data sharing in neuroimaging , 2014, Nature Neuroscience.

[59]  S. Frick,et al.  Compressed Sensing , 2014, Computer Vision, A Reference Guide.

[60]  Hanchuan Peng,et al.  TeraFly: real-time three-dimensional visualization and annotation of terabytes of multidimensional volumetric images , 2016, Nature Methods.

[61]  Mark Ellisman,et al.  e-Neuroscience: challenges and triumphs in integrating distributed data from molecules to brains , 2004, Nature Neuroscience.

[62]  Liuqing Yang,et al.  Where does AlphaGo go: from church-turing thesis to AlphaGo thesis and beyond , 2016, IEEE/CAA Journal of Automatica Sinica.

[63]  James G. King,et al.  Reconstruction and Simulation of Neocortical Microcircuitry , 2015, Cell.

[64]  M. F. Huerta,et al.  Neuroinformatics : An Overview of the Human Brain Project , 2013 .

[65]  Nancy Y. Ip,et al.  China Brain Project: Basic Neuroscience, Brain Diseases, and Brain-Inspired Computing , 2016, Neuron.

[66]  Bertram Ludäscher,et al.  Knowledge-based integration of neuroscience data sources , 2000, Proceedings. 12th International Conference on Scientific and Statistica Database Management.

[67]  Li Fei-Fei,et al.  ImageNet: A large-scale hierarchical image database , 2009, CVPR.

[68]  Alois Knoll,et al.  The Human Brain Project: Creating a European Research Infrastructure to Decode the Human Brain , 2016, Neuron.

[69]  Allan R. Jones,et al.  A mesoscale connectome of the mouse brain , 2014, Nature.

[70]  Yuan-Gui Zhu,et al.  Grand Research Plan for Neural Circuits of Emotion and Memory — Current status of neural circuit studies in China , 2013, Neuroscience Bulletin.

[71]  Stephen D. Larson,et al.  OpenWorm: an open-science approach to modeling Caenorhabditis elegans , 2014, Front. Comput. Neurosci..

[72]  Arthur W. Toga,et al.  Digital Atlases as a Framework for Data Sharing , 2008, Front. Neurosci..

[73]  Hui Li,et al.  Endomorphin-2 Decreases Excitatory Synaptic Transmission in the Spinal Ventral Horn of the Rat , 2017, Front. Neural Circuits.

[74]  Justus M. Kebschull,et al.  The logic of single-cell projections from visual cortex , 2018, Nature.

[75]  Esther Landhuis,et al.  Neuroscience: Big brain, big data , 2017, Nature.

[76]  Mu-ming Poo,et al.  Towards brain-inspired artificial intelligence , 2018, National Science Review.

[77]  Franz Pfeiffer,et al.  High-resolution tomographic imaging of microvessels , 2008, Optical Engineering + Applications.