神经元形态重建工具的研究进展
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摘要
近年来,分子标记和显微光学成像技术的系列突破,使得单细胞分辨的全脑尺度神经群落成像成为现实.然而,现有神经元形态重建工具的发展速度远远滞后于海量数据的产生速度,难以满足现阶段成像数据的分析需求.在此背景下,我们首先分析了神经元形态重建工具发展滞后的原因,简述现有半自动和全自动神经元形态重建工具的特点和最新发展,并结合现有工具的特点分析其向高通量、高准确度重建工具发展时面临的挑战.最后,我们对未来形态重建工具的发展趋势及应用前景做出展望.
Recent breakthroughs in molecular labeling and light microscopy enable the imaging of brain-wide neuronal population at cellular level. However, the development of neuronal reconstruction tools lags far behind massive datasets generation, which fails to meet the data analysis requirement at the current stage. In this sense,we first sought reasons for backwardness in current reconstruction tools and we summarized the features and introduced latest developments in these semi-automatic and fully automatic tools. Based on the summarized features, we further listed the challenges in developing reconstruction tools with high throughput and accuracy. In the end, we aired our views on the future development and application prospect of tools in neuron reconstruction.
Recent breakthroughs in molecular labeling and light microscopy enable the imaging of brain-wide neuronal population at cellular level. However, the development of neuronal reconstruction tools lags far behind massive datasets generation, which fails to meet the data analysis requirement at the current stage. In this sense,we first sought reasons for backwardness in current reconstruction tools and we summarized the features and introduced latest developments in these semi-automatic and fully automatic tools. Based on the summarized features, we further listed the challenges in developing reconstruction tools with high throughput and accuracy. In the end, we aired our views on the future development and application prospect of tools in neuron reconstruction.
引文
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[17]Gong H,Xu D,Yuan J,et al.High-throughput dual-colour precision imaging for brain-wide connectome with cytoarchitectonic landmarks at the cellular level.Nat.Commu.,2016,7:12142
[18]Cyranoski D.China launches brain-imaging factory.Nat News,2017,548(7667):268-269
[19]Meijering E.Neuron tracing in perspective.Cytometry A,2010,77(7):693-704
[20]Ascoli G A.Sharing neuron data:carrots,sticks,and digital records.Plos Biol.,2015,13(10):e1002275
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[22]Helmstaedter M.Cellular-resolution connectomics:challenges of dense neural circuit reconstruction.Nat Methods,2013,10(6):501-507
[23]Wang Y,Narayanaswamy A,Tsai C L,et al.A broadly applicable 3-D neuron tracing method based on open-curve snake.Neuroinformatics,2011,9(2-3):193-217
[24]Gillette T A,Brown K M,Svoboda K,et al.DIADEMchallenge.Org:A compendium of resources fostering the continuous development of automated neuronal reconstruction.Neuroinformatics,2011,9(2-3):303-304
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[26]Peng H,Meijering E,Ascoli G A.From DIADEM to Big Neuron.Neuroinformatics,2015,13(3):259-260
[27]Peng H,Hawrylycz M,Roskams J,et al.Big Neuron:Large-scale3D neuron reconstruction from optical microscopy images.Neuron,2015,87(2):252-256
[28]Shen H.Neuron encyclopaedia fires up to reveal brain secrets:but effort to catalogue brain's building blocks may stoke disagreements over classification.Nature,2015,520(7545):13-15
[29]Kim J,Zhao T,Petralia R S,et al.m GRASP enables mapping mammalian synaptic connectivity with light microscopy.Nat Methods,2011,9(1):96-102
[30]Feng L,Zhao T,Kim J.neu Tube 1.0:a new design for efficient neuron reconstruction software based on the SWC format.Eneuro,2015,2(1):0049-14
[31]Xiao H,Peng H.APP2:automatic tracing of 3D neuron morphology based on hierarchical pruning of a gray-weighted image distance-tree.Bioinformatics,2013,29(11):1448-1454
[32]Quan T,Zhou H,Li J,et al.Neuro GPS-Tree:automatic reconstruction of large-scale neuronal populations with dense neurites.Nat Methods,2016,13(1):51-54
[33]Hart P E,Nilsson N J,Raphael B.A formal basis for the heuristic determination of minimum cost paths.IEEE Trans Syst Sci Cybern,1968,4(2):100-107
[34]Sato Y,Nakajima S,Shiraga N,et al.Three-dimensional multiscale line filter for segmentation and visualization of curvilinear structures in medical images.Med Image Anal,1998,2(2):143-168
[35]Glaser J R,Glaser E M.Neuron imaging with Neurolucida-a PC-based system for image combining microscopy.Comput Med Imag Grap,1990,14(5):307-317
[36]Stalling D,Westerhoff M,Hege H C.Amira:a highly interactive system for visual data analysis.The Visualization Handbook,2005,38:749-767
[37]http://www.bitplane.com/imaris/filamenttracer
[38]Meijering E,Jacob M,Sarria J C,et al.Design and validation of a tool for neurite tracing and analysis in fluorescence microscopy images.Cytometry A,2004,58(2):167-176
[39]Brown K M,Donohue D E,D'alessandro G,et al.A cross-platform freeware tool for digital reconstruction of neuronal arborizations from image stacks.Neuroinformatics,2005,3(4):343-359
[40]Longair M H,Baker D A,Armstrong J D.Simple neurite tracer:open source software for reconstruction,visualization and analysis of neuronal processes.Bioinformatics,2011,27(17):2453-2454
[41]Magliaro C,Callara A L,Vanello N,et al.A manual segmentation tool for three-dimensional neuron datasets.Front.Neuroinform.,2017,11:36
[42]Zhao T,Xie J,Amat F,et al.Automated reconstruction of neuronal morphology based on local geometrical and global structural models.Neuroinformatics,2011,9(2-3):247-261
[43]Peng H,Long F,Myers G.Automatic 3D neuron tracing using allpath pruning.Bioinformatics,2011,27(13):i239-247
[44]Turetken E,Gonzalez G,Blum C,et al.Automated reconstruction of dendritic and axonal trees by global optimization with geometric priors.Neuroinformatics,2011,9(2-3):279-302
[45]Xu C,Prince J L.Snakes,shapes,and gradient vector flow.IEEETrans Image Processing,1998,7(3):359-369
[46]Gala R,Chapeton J,Jitesh J,et al.Active learning of neuron morphology for accurate automated tracing of neurites.Front.Neuroanat.,2014,8:37
[47]Wearne S,Rodriguez A,Ehlenberger D,et al.New techniques for imaging,digitization and analysis of three-dimensional neural morphology on multiple scales.Neuroscience,2005,136(3):661-680
[48]Skibbe H,Reisert M,Nakae K,et al.PAT-probabilistic axon tracking for densely labeled neurons in large 3D micrographs.IEEE Trans Med Img,2018,38(1):69-78
[49]Radojevic M,Meijering E.Automated neuron tracing using probability hypothesis density filtering.Bioinformatics,2017,33(7):1073-1080
[50]Zhou Z,Kuo H-C,Peng H,et al.Deep Neuron:an open deep learning toolbox for neuron tracing.Brain informatics,2018,5(2):3-12
[51]Li R,Zeng T,Peng H,et al.Deep learning segmentation of optical microscopy images improves 3-D neuron reconstruction.IEEETrans Med Imag,2017,36(7):1533-1541
[52]Acciai L,Soda P,Iannello G.Automated neuron tracing methods:an updated account.Neuroinformatics,2016,14(4):353-367
[53]Ong K H,De J,Cheng L,et al.Neuron Cyto II:an automatic and quantitative solution for crossover neural cells in high throughput screening.Cytometry A,2016,89(8):747-754
[54]Peng H,Ruan Z,Long F,et al.V3D enables real-time 3Dvisualization and quantitative analysis of large-scale biological image data sets.Nat Biotechnol,2010,28(4):348-353
[55]Rodriguez A,Ehlenberger D B,Hof P R,et al.Three-dimensional neuron tracing by voxel scooping.J.Neurosci.Methods,2009,184(1):169-175
[56]Adams R,Bischof L.Seeded region growing.IEEE Trans Pattern Analy.Machine Intell,1994,16(6):641-647
[57]Fiala J C.Reconstruct:a free editor for serial section microscopy.JMicrosc,2005,218(1):52-61
[58]Rodriguez A,Ehlenberger D B,Dickstein D L,et al.Automated three-dimensional detection and shape classification of dendritic spines from fluorescence microscopy images.Plos One,2008,3(4):e1997
[59]Li S,Zhou H,Quan T,et al.Sparse Tracer:the reconstruction of discontinuous neuronal morphology in noisy images.Neuroinformatics,2016,15(2):133-149
[60]Kass M,Witkin A,Terzopoulos D.Snakes:active contour models.Int J Comput Vision,1988,1(4):321-331
[61]Caselles V,Kimmel R,Sapiro G.Geodesic active contours.Int JComput Vision,1997,22(1):61-79
[62]Chan T F,Vese L A.Active contours without edges.IEEE Trans Image Processing,2001,10(2):266-277
[63]Schmitt S,Evers J F,Duch C,et al.New methods for the computerassisted 3D reconstruction of neurons from confocal image stacks.Neuro Image,2004,23(4):1283-1298
[64]Vasilkoski Z,Stepanyants A.Detection of the optimal neuron traces in confocal microscopy images.J Neurosci Methods,2009,178(1):197-204
[65]Dijkstra E W.A note on two problems in connexion with graphs.Numer Math,1959,1(1):269-271
[66]Cohen L D,Kimmel R.Global minimum for active contour models:a minimal path approach.Int J Comput Vision,1997,24(1):57-78
[67]Bria A,Iannello G,Onofri L,et al.Tera Fly:real-time threedimensional visualization and annotation of terabytes of multidimensional volumetric images.Nat Methods,2016,13(3):192-194
[68]Wang C W,Lee Y C,Pradana H,et al.Ensemble neuron tracer for3D neuron reconstruction.Neuroinformatics,2017,15(2):1-14
[69]Chen H,Xiao H,Liu T,et al.Smart Tracing:self-learning-based neuron reconstruction.Brain Informatics,2015,2(3):135-144
[70]Megjhani M,Rey-Villamizar N,Merouane A,et al.Populationscale three-dimensional reconstruction and quantitative profiling of microglia arbors.Bioinformatics,2015,31(13):2190-2198
[71]Becker C,Rigamonti R,Lepetit V,et al.Supervised feature learning for curvilinear structure segmentation.In MICCAI,2013,16:526-533
[2]Donohue D E,Ascoli G A.Automated reconstruction of neuronal morphology:an overview.Brain Res Rev,2011,67(1-2):94-102
[3]Svoboda K.The past,present,and future of single neuron reconstruction.Neuroinformatics,2011,9(2-3):97-98
[4]Lu J.Neuronal tracing for connectomic studies.Neuroinformatics,2011,9(2-3):159-166
[5]骆清铭.脑空间信息学--连接脑科学与类脑人工智能的桥梁.中国科学:生命科学,2017,47:1015-1024Luo Q M.Sci China Life Sci,2017,47:1015-1024
[6]Myatt D R,Hadlington T,Ascoli G A,et al.Neuromantic-from semi-manual to semi-automatic reconstruction of neuron morphology.Front Neuroinform,2012,6:4
[7]Jefferis G S,Livet J.Sparse and combinatorial neuron labelling.Curr Opin Neurobiol,2012,22(1):101-110
[8]Weitzman M D,Linden R M.Adeno-associated virus biology.Methods Mol Biol,2011,807:1-23
[9]Li A,Gong H,Zhang B,et al.Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain.Science,2010,330(6009):1404-1408
[10]Ragan T,Kadiri L R,Venkataraju K U,et al.Serial two-photon tomography for automated ex vivo mouse brain imaging.Nat Methods,2012,9(3):255-258
[11]Silvestri L,Bria A,Sacconi L,et al.Confocal light sheet microscopy:micron-scale neuroanatomy of the entire mouse brain.Opt Express,2012,20(18):20582-20598
[12]Liu S,Nie J,Li Y,et al.Three-dimensional,isotropic imaging of mouse brain using multi-view deconvolution light sheet microscopy.J Innov Opt Heal Sci,2017,10(05):1743006
[13]杜久林,毕国强,骆清铭,等.脑科学研究新技术.中国科学院院刊,2016,31(7):783-792Du J L,Bi G Q,Luo Q M,et al.Bulletin of the Chinese Academy of Sciences,2016,31(7):783-792
[14]Osten P,Margrie T W.Mapping brain circuitry with a light microscope.Nat Methods,2013,10(6):515-523
[15]Economon M N,Clack N G,Levis L D,et al.A platform for brainwide imaging and reconstruction of individual neurons.Elife,2016,5
[16]Gong H,Zeng S,Yan C,et al.Continuously tracing brain-wide long-distance axonal projections in mice at a one-micron voxel resolution.Neuroimage,2013,74:87-98
[17]Gong H,Xu D,Yuan J,et al.High-throughput dual-colour precision imaging for brain-wide connectome with cytoarchitectonic landmarks at the cellular level.Nat.Commu.,2016,7:12142
[18]Cyranoski D.China launches brain-imaging factory.Nat News,2017,548(7667):268-269
[19]Meijering E.Neuron tracing in perspective.Cytometry A,2010,77(7):693-704
[20]Ascoli G A.Sharing neuron data:carrots,sticks,and digital records.Plos Biol.,2015,13(10):e1002275
[21]Lichtman J W,Denk W.The big and the small:challenges of imaging the brain's circuits.Science,2011,334(6056):618-623
[22]Helmstaedter M.Cellular-resolution connectomics:challenges of dense neural circuit reconstruction.Nat Methods,2013,10(6):501-507
[23]Wang Y,Narayanaswamy A,Tsai C L,et al.A broadly applicable 3-D neuron tracing method based on open-curve snake.Neuroinformatics,2011,9(2-3):193-217
[24]Gillette T A,Brown K M,Svoboda K,et al.DIADEMchallenge.Org:A compendium of resources fostering the continuous development of automated neuronal reconstruction.Neuroinformatics,2011,9(2-3):303-304
[25]Liu Y.The DIADEM and beyond.Neuroinformatics,2011,9(2):99-102
[26]Peng H,Meijering E,Ascoli G A.From DIADEM to Big Neuron.Neuroinformatics,2015,13(3):259-260
[27]Peng H,Hawrylycz M,Roskams J,et al.Big Neuron:Large-scale3D neuron reconstruction from optical microscopy images.Neuron,2015,87(2):252-256
[28]Shen H.Neuron encyclopaedia fires up to reveal brain secrets:but effort to catalogue brain's building blocks may stoke disagreements over classification.Nature,2015,520(7545):13-15
[29]Kim J,Zhao T,Petralia R S,et al.m GRASP enables mapping mammalian synaptic connectivity with light microscopy.Nat Methods,2011,9(1):96-102
[30]Feng L,Zhao T,Kim J.neu Tube 1.0:a new design for efficient neuron reconstruction software based on the SWC format.Eneuro,2015,2(1):0049-14
[31]Xiao H,Peng H.APP2:automatic tracing of 3D neuron morphology based on hierarchical pruning of a gray-weighted image distance-tree.Bioinformatics,2013,29(11):1448-1454
[32]Quan T,Zhou H,Li J,et al.Neuro GPS-Tree:automatic reconstruction of large-scale neuronal populations with dense neurites.Nat Methods,2016,13(1):51-54
[33]Hart P E,Nilsson N J,Raphael B.A formal basis for the heuristic determination of minimum cost paths.IEEE Trans Syst Sci Cybern,1968,4(2):100-107
[34]Sato Y,Nakajima S,Shiraga N,et al.Three-dimensional multiscale line filter for segmentation and visualization of curvilinear structures in medical images.Med Image Anal,1998,2(2):143-168
[35]Glaser J R,Glaser E M.Neuron imaging with Neurolucida-a PC-based system for image combining microscopy.Comput Med Imag Grap,1990,14(5):307-317
[36]Stalling D,Westerhoff M,Hege H C.Amira:a highly interactive system for visual data analysis.The Visualization Handbook,2005,38:749-767
[37]http://www.bitplane.com/imaris/filamenttracer
[38]Meijering E,Jacob M,Sarria J C,et al.Design and validation of a tool for neurite tracing and analysis in fluorescence microscopy images.Cytometry A,2004,58(2):167-176
[39]Brown K M,Donohue D E,D'alessandro G,et al.A cross-platform freeware tool for digital reconstruction of neuronal arborizations from image stacks.Neuroinformatics,2005,3(4):343-359
[40]Longair M H,Baker D A,Armstrong J D.Simple neurite tracer:open source software for reconstruction,visualization and analysis of neuronal processes.Bioinformatics,2011,27(17):2453-2454
[41]Magliaro C,Callara A L,Vanello N,et al.A manual segmentation tool for three-dimensional neuron datasets.Front.Neuroinform.,2017,11:36
[42]Zhao T,Xie J,Amat F,et al.Automated reconstruction of neuronal morphology based on local geometrical and global structural models.Neuroinformatics,2011,9(2-3):247-261
[43]Peng H,Long F,Myers G.Automatic 3D neuron tracing using allpath pruning.Bioinformatics,2011,27(13):i239-247
[44]Turetken E,Gonzalez G,Blum C,et al.Automated reconstruction of dendritic and axonal trees by global optimization with geometric priors.Neuroinformatics,2011,9(2-3):279-302
[45]Xu C,Prince J L.Snakes,shapes,and gradient vector flow.IEEETrans Image Processing,1998,7(3):359-369
[46]Gala R,Chapeton J,Jitesh J,et al.Active learning of neuron morphology for accurate automated tracing of neurites.Front.Neuroanat.,2014,8:37
[47]Wearne S,Rodriguez A,Ehlenberger D,et al.New techniques for imaging,digitization and analysis of three-dimensional neural morphology on multiple scales.Neuroscience,2005,136(3):661-680
[48]Skibbe H,Reisert M,Nakae K,et al.PAT-probabilistic axon tracking for densely labeled neurons in large 3D micrographs.IEEE Trans Med Img,2018,38(1):69-78
[49]Radojevic M,Meijering E.Automated neuron tracing using probability hypothesis density filtering.Bioinformatics,2017,33(7):1073-1080
[50]Zhou Z,Kuo H-C,Peng H,et al.Deep Neuron:an open deep learning toolbox for neuron tracing.Brain informatics,2018,5(2):3-12
[51]Li R,Zeng T,Peng H,et al.Deep learning segmentation of optical microscopy images improves 3-D neuron reconstruction.IEEETrans Med Imag,2017,36(7):1533-1541
[52]Acciai L,Soda P,Iannello G.Automated neuron tracing methods:an updated account.Neuroinformatics,2016,14(4):353-367
[53]Ong K H,De J,Cheng L,et al.Neuron Cyto II:an automatic and quantitative solution for crossover neural cells in high throughput screening.Cytometry A,2016,89(8):747-754
[54]Peng H,Ruan Z,Long F,et al.V3D enables real-time 3Dvisualization and quantitative analysis of large-scale biological image data sets.Nat Biotechnol,2010,28(4):348-353
[55]Rodriguez A,Ehlenberger D B,Hof P R,et al.Three-dimensional neuron tracing by voxel scooping.J.Neurosci.Methods,2009,184(1):169-175
[56]Adams R,Bischof L.Seeded region growing.IEEE Trans Pattern Analy.Machine Intell,1994,16(6):641-647
[57]Fiala J C.Reconstruct:a free editor for serial section microscopy.JMicrosc,2005,218(1):52-61
[58]Rodriguez A,Ehlenberger D B,Dickstein D L,et al.Automated three-dimensional detection and shape classification of dendritic spines from fluorescence microscopy images.Plos One,2008,3(4):e1997
[59]Li S,Zhou H,Quan T,et al.Sparse Tracer:the reconstruction of discontinuous neuronal morphology in noisy images.Neuroinformatics,2016,15(2):133-149
[60]Kass M,Witkin A,Terzopoulos D.Snakes:active contour models.Int J Comput Vision,1988,1(4):321-331
[61]Caselles V,Kimmel R,Sapiro G.Geodesic active contours.Int JComput Vision,1997,22(1):61-79
[62]Chan T F,Vese L A.Active contours without edges.IEEE Trans Image Processing,2001,10(2):266-277
[63]Schmitt S,Evers J F,Duch C,et al.New methods for the computerassisted 3D reconstruction of neurons from confocal image stacks.Neuro Image,2004,23(4):1283-1298
[64]Vasilkoski Z,Stepanyants A.Detection of the optimal neuron traces in confocal microscopy images.J Neurosci Methods,2009,178(1):197-204
[65]Dijkstra E W.A note on two problems in connexion with graphs.Numer Math,1959,1(1):269-271
[66]Cohen L D,Kimmel R.Global minimum for active contour models:a minimal path approach.Int J Comput Vision,1997,24(1):57-78
[67]Bria A,Iannello G,Onofri L,et al.Tera Fly:real-time threedimensional visualization and annotation of terabytes of multidimensional volumetric images.Nat Methods,2016,13(3):192-194
[68]Wang C W,Lee Y C,Pradana H,et al.Ensemble neuron tracer for3D neuron reconstruction.Neuroinformatics,2017,15(2):1-14
[69]Chen H,Xiao H,Liu T,et al.Smart Tracing:self-learning-based neuron reconstruction.Brain Informatics,2015,2(3):135-144
[70]Megjhani M,Rey-Villamizar N,Merouane A,et al.Populationscale three-dimensional reconstruction and quantitative profiling of microglia arbors.Bioinformatics,2015,31(13):2190-2198
[71]Becker C,Rigamonti R,Lepetit V,et al.Supervised feature learning for curvilinear structure segmentation.In MICCAI,2013,16:526-533
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