[1] Petreanu L, Mao T Y, Sternson S M et al. The subcellular organization of neocortical excitatory connections[J]. Nature, 457, 1142-1145(2009).

[2] Miyamichi K, Amat F, Moussavi F et al. Cortical representations of olfactory input by trans-synaptic tracing[J]. Nature, 472, 191-196(2011).

[3] Koch C, Reid R C. Observatories of the mind[J]. Nature, 483, 397-398(2012).

[4] Snyder E Y, Yoon C, Flax J D et al. Multipotent neural precursors can differentiate toward replacement of neurons undergoing targeted apoptotic degeneration in adult mouse neocortex[J]. Proceedings of the National Academy of Sciences of the United States of America, 94, 11663-11668(1997).

[5] Helmchen F, Denk W. Deep tissue two-photon microscopy[J]. Nature Methods, 2, 932-940(2005).

[6] Conchello J A, Lichtman J W. Optical sectioning microscopy[J]. Nature Methods, 2, 920-931(2005).

[7] Mertz J. Optical sectioning microscopy with planar or structured illumination[J]. Nature Methods, 8, 811-819(2011).

[8] Wang X, Tu S J, Liu X et al. Advance and prospect for three-dimensional super-resolution microscopy[J]. Laser & Optoelectronics Progress, 58, 2200001(2021).

[9] Liu Z, Luo Z W, Wang Z Y et al. Super-resolution fluorescence microscopy image reconstruction algorithm based on structured illumination[J]. Chinese Journal of Lasers, 48, 0307001(2021).

[10] Li H Y, Qu L Y, Hua Z J et al. Deep learning based fluorescence microscopy imaging technologies and applications[J]. Laser & Optoelectronics Progress, 58, 1811007(2021).

[11] Poo M M, Du J L, Ip N Y et al. China brain project: basic neuroscience, brain diseases, and brain-inspired computing[J]. Neuron, 92, 591-596(2016).

[12] Osten P, Margrie T W. Mapping brain circuitry with a light microscope[J]. Nature Methods, 10, 515-523(2013).

[13] Guo C D, Long B, Hu Y R et al. Early-stage reduction of the dendritic complexity in basolateral amygdala of a transgenic mouse model of Alzheimer’s disease[J]. Biochemical and Biophysical Research Communications, 486, 679-685(2017).

[14] Guo C D, Peng J, Zhang Y L et al. Single-axon level morphological analysis of corticofugal projection neurons in mouse barrel field[J]. Scientific Reports, 7, 2846(2017).

[15] Winnubst J, Bas E, Ferreira T A et al. Reconstruction of 1,000 projection neurons reveals new cell types and organization of long-range connectivity in the mouse brain[J]. Cell, 179, 268-281(2019).

[16] Peng H C, Xie P, Liu L J et al. Morphological diversity of single neurons in molecularly defined cell types[J]. Nature, 598, 174-181(2021).

[17] Wang Q X, Ding S L, Li Y et al. The Allen mouse brain common coordinate framework: a 3D reference atlas[J]. Cell, 181, 936-953(2020).

[18] Long B, Jiang T, Zhang J M et al. Mapping the architecture of ferret brains at single-cell resolution[J]. Frontiers in Neuroscience, 14, 322(2020).

[19] Qu L, Li Y Y, Xie P et al. Cross-modal coherent registration of whole mouse brains[J]. Nature Methods, 19, 111-118(2022).

[20] Feng Z, Li A A, Gong H et al. Constructing the rodent stereotaxic brain atlas: a survey[J]. Science China Life Sciences, 65, 93-106(2022).

[21] Wu J P, He Y, Yang Z Q et al. 3D BrainCV: simultaneous visualization and analysis of cells and capillaries in a whole mouse brain with one-micron voxel resolution[J]. NeuroImage, 87, 199-208(2014).

[22] Wu J P, Guo C D, Chen S B et al. Direct 3D analyses reveal barrel-specific vascular distribution and cross-barrel branching in the mouse barrel cortex[J]. Cerebral Cortex, 26, 23-31(2014).

[23] Xiong B Y, Li A A, Lou Y et al. Precise cerebral vascular atlas in stereotaxic coordinates of whole mouse brain[J]. Frontiers in Neuroanatomy, 11, 128(2017).

[24] Zhang X C, Yin X Z, Zhang J J et al. High-resolution mapping of brain vasculature and its impairment in the hippocampus of Alzheimer’s disease mice[J]. National Science Review, 6, 1223-1238(2019).

[25] Tang J, Zhu H, Tian X Y et al. Extension of endocardium-derived vessels generate coronary arteries in neonates[J]. Circulation Research, 130, 352-365(2022).

[26] Yin X Z, Zhang X C, Zhang J J et al. High-resolution digital panorama of multiple structures in whole brain of Alzheimer’s disease mice[J]. Frontiers in Neuroscience, 16, 870520(2022).

[27] He X Z, Li X, Li Z H et al. High-resolution 3D demonstration of regional heterogeneity in the glymphatic system[J]. Journal of Cerebral Blood Flow and Metabolism, 42, 2017-2031(2022).

[28] Oh S W, Harris J A, Ng L et al. A mesoscale connectome of the mouse brain[J]. Nature, 508, 207-214(2014).

[29] Callaway E M, Dong H W, Ecker J R et al. A multimodal cell census and atlas of the mammalian primary motor cortex[J]. Nature, 598, 86-102(2021).

[30] Muñoz-Castañeda R, Zingg B, Matho K S et al. Cellular anatomy of the mouse primary motor cortex[J]. Nature, 598, 159-166(2021).

[31] Foster N N, Barry J, Korobkova L et al. The mouse cortico-basal ganglia-thalamic network[J]. Nature, 598, 188-194(2021).

[32] Xu Z C, Feng Z, Zhao M T et al. Whole-brain connectivity atlas of glutamatergic and gabaergic neurons in the mouse dorsal and median raphe nuclei[J]. eLife, 10, e65502(2021).

[33] Sun Q T, Zhang J P, Li A A et al. Acetylcholine deficiency disrupts extratelencephalic projection neurons in the prefrontal cortex in a mouse model of Alzheimer’s disease[J]. Nature Communications, 13, 998(2022).

[34] Richardson D S, Lichtman J W. Clarifying tissue clearing[J]. Cell, 162, 246-257(2015).

[35] Richardson D S, Guan W, Matsumoto K et al. Tissue clearing[J]. Nature Reviews Methods Primers, 1, 84(2021).

[36] Tainaka K, Kuno A, Kubota S I et al. Chemical principles in tissue clearing and staining protocols for whole-body cell profiling[J]. Annual Review of Cell and Developmental Biology, 32, 713-741(2016).

[37] Susaki E A, Ueda H R. Whole-body and whole-organ clearing and imaging techniques with single-cell resolution: toward organism-level systems biology in mammals[J]. Cell Chemical Biology, 23, 137-157(2016).

[38] Spalteholz W[Z]. Über das durchsichtigmachen von menschlichen und tierischen Präparaten und seine theoretischen Bedingungen, nebstanhang: über knochenfärbung(1914).

[39] Ueda H R, Ertürk A, Chung K et al. Tissue clearing and its applications in neuroscience[J]. Nature Reviews Neuroscience, 21, 61-79(2020).

[40] Ertürk A, Becker K, Jährling N et al. Three-dimensional imaging of solvent-cleared organs using 3DISCO[J]. Nature Protocols, 7, 1983-1995(2012).

[41] Ertürk A, Mauch C P, Hellal F et al. Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury[J]. Nature Medicine, 18, 166-171(2012).

[42] Renier N, Wu Z H, Simon DJ et al. iDISCO: a simple, rapid method to immunolabel large tissue samples for volume imaging[J]. Cell, 159, 896-910(2014).

[43] Pan C C, Cai R Y, Quacquarelli F P et al. Shrinkage-mediated imaging of entire organs and organisms using uDISCO[J]. Nature Methods, 13, 859-867(2016).

[44] Qi Y S, Yu T T, Xu J Y et al. FDISCO: advanced solvent-based clearing method for imaging whole organs[J]. Science Advances, 5, eaau8355(2019).

[45] Cai R Y, Pan C C, Ghasemigharagoz A et al. Panoptic imaging of transparent mice reveals whole-body neuronal projections and skull-meninges connections[J]. Nature Neuroscience, 22, 317-327(2019).

[46] Hahn C, Becker K, Saghafi S et al. High-resolution imaging of fluorescent whole mouse brains using stabilised organic media (sDISCO)[J]. Journal of Biophotonics, 12, e201800368(2019).

[47] Jing D, Zhang S W, Luo W J et al. Tissue clearing of both hard and soft tissue organs with the PEGASOS method[J]. Cell Research, 28, 803-818(2018).

[48] Ke M T, Fujimoto S, Imai T. SeeDB: a simple and morphology-preserving optical clearing agent for neuronal circuit reconstruction[J]. Nature Neuroscience, 16, 1154-1161(2013).

[49] Ke M T, Nakai Y, Fujimoto S et al. Super-resolution mapping of neuronal circuitry with an index-optimized clearing agent[J]. Cell Reports, 14, 2718-2732(2016).

[50] Liu Y C, Chiang A S. High-resolution confocal imaging and three-dimensional rendering[J]. Methods, 30, 86-93(2003).

[51] Aoyagi Y, Kawakami R, Osanai H et al. A rapid optical clearing protocol using 2,2'-thiodiethanol for microscopic observation of fixed mouse brain[J]. PLoS One, 10, e0116280(2015).

[52] Zhu X P, Huang L M, Zheng Y et al. Ultrafast optical clearing method for three-dimensional imaging with cellular resolution[J]. Proceedings of the National Academy of Sciences of the United States of America, 116, 11480-11489(2019).

[53] Hama H, Kurokawa H, Kawano H et al. Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain[J]. Nature Neuroscience, 14, 1481-1488(2011).

[54] Hama H, Hioki H, Namiki K et al. ScaleS: an optical clearing palette for biological imaging[J]. Nature Neuroscience, 18, 1518-1529(2015).

[55] Yu T T, Zhu J T, Li Y S et al. RTF: a rapid and versatile tissue optical clearing method[J]. Scientific Reports, 8, 1964(2018).

[56] Hou B, Zhang D, Zhao S et al. Scalable and DiI-compatible optical clearance of the mammalian brain[J]. Frontiers in Neuroanatomy, 9, 19(2015).

[57] Chen L L, Li G Y, Li Y M et al. UbasM: an effective balanced optical clearing method for intact biomedical imaging[J]. Scientific Reports, 7, 12218(2017).

[58] Susaki E A, Tainaka K, Perrin D et al. Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis[J]. Cell, 157, 726-739(2014).

[59] Susaki E A, Tainaka K, Perrin D et al. Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging[J]. Nature Protocols, 10, 1709-1727(2015).

[60] Chung K, Wallace J, Kim S Y et al. Structural and molecular interrogation of intact biological systems[J]. Nature, 497, 332-337(2013).

[61] Yang B, Treweek J B, Kulkarni R P et al. Single-cell phenotyping within transparent intact tissue through whole-body clearing[J]. Cell, 158, 945-958(2014).

[62] Treweek J B, Chan K Y, Flytzanis N C et al. Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping[J]. Nature Protocols, 10, 1860-1896(2015).

[63] Yu T T, Qi Y S, Zhu J T et al. Elevated-temperature-induced acceleration of PACT clearing process of mouse brain tissue[J]. Scientific Reports, 7, 38848(2017).

[64] Perbellini F, Liu A K L, Watson S A et al. Free-of-acrylamide SDS-based tissue clearing (FASTClear) for three dimensional visualization of myocardial tissue[J]. Scientific Reports, 7, 5188(2017).

[65] Murray E, Cho J H, Goodwin D et al. Simple, scalable proteomic imaging for high-dimensional profiling of intact systems[J]. Cell, 163, 1500-1514(2015).

[66] Park Y G, Sohn C H, Chen R et al. Protection of tissue physicochemical properties using polyfunctional crosslinkers[J]. Nature Biotechnology, 37, 73-83(2019).

[67] Krzic U, Gunther S, Saunders T E et al. Multiview light-sheet microscope for rapid in toto imaging[J]. Nature Methods, 9, 730-733(2012).

[68] Chhetri R K, Amat F, Wan Y N et al. Whole-animal functional and developmental imaging with isotropic spatial resolution[J]. Nature Methods, 12, 1171-1178(2015).

[69] Nie J, Liu S, Yu T T et al. Fast, 3D isotropic imaging of whole mouse brain using multiangle-resolved subvoxel SPIM[J]. Advanced Science, 7, 1901891(2019).

[70] Swoger J, Verveer P, Greger K et al. Multi-view image fusion improves resolution in three-dimensional microscopy[J]. Optics Express, 15, 8029-8042(2007).

[71] Preibisch S, Amat F, Stamataki E et al. Efficient Bayesian-based multiview deconvolution[J]. Nature Methods, 11, 645-648(2014).

[72] Siedentopf H, Zsigmondy R. Uber sichtbarmachung und größenbestimmung ultramikoskopischer teilchen, mit besonderer anwendung auf goldrubingläser[J]. Annalen Der Physik, 315, 1-39(1902).

[73] Huisken J, Swoger J, del Bene F et al. Optical sectioning deep inside live embryos by selective plane illumination microscopy[J]. Science, 305, 1007-1009(2004).

[74] Dodt H U, Leischner U, Schierloh A et al. Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain[J]. Nature Methods, 4, 331-336(2007).

[75] Keller P J, Schmidt A D, Wittbrodt J et al. Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy[J]. Science, 322, 1065-1069(2008).

[76] Silvestri L, Bria A, Sacconi L et al. Confocal light sheet microscopy: micron-scale neuroanatomy of the entire mouse brain[J]. Optics Express, 20, 20582-20598(2012).

[77] Baumgart E, Kubitscheck U. Scanned light sheet microscopy with confocal slit detection[J]. Optics Express, 20, 21805-21814(2012).

[78] Chakraborty T, Driscoll M K, Jeffery E et al. Light-sheet microscopy of cleared tissues with isotropic, subcellular resolution[J]. Nature Methods, 16, 1109-1113(2019).

[79] Glaser A K, Bishop K W, Barner L A et al. A hybrid open-top light-sheet microscope for versatile multi-scale imaging of cleared tissues[J]. Nature Methods, 19, 613-619(2022).

[80] Chen Y L, Li X L, Zhang D D et al. A versatile tiling light sheet microscope for imaging of cleared tissues[J]. Cell Reports, 33, 108349(2020).

[81] Gao L. Extend the field of view of selective plan illumination microscopy by tiling the excitation light sheet[J]. Optics Express, 23, 6102-6111(2015).

[82] Wang H, Zhu Q Y, Ding L F et al. Scalable volumetric imaging for ultrahigh-speed brain mapping at synaptic resolution[J]. National Science Review, 6, 982-992(2019).

[83] Xu F, Shen Y, Ding L F et al. High-throughput mapping of a whole rhesus monkey brain at micrometer resolution[J]. Nature Biotechnology, 39, 1521-1528(2021).

[84] Zhang Z Z, Yao X, Yin X X et al. Multi-scale light-sheet fluorescence microscopy for fast whole brain imaging[J]. Frontiers in Neuroanatomy, 15, 732464(2021).

[85] Ragan T, Sylvan J D, Kim K H et al. High-resolution whole organ imaging using two-photon tissue cytometry[J]. Journal of Biomedical Optics, 12, 014015(2007).

[86] Ragan T, Kadiri L R, Venkataraju K U et al. Serial two-photon tomography for automated ex vivo mouse brain imaging[J]. Nature Methods, 9, 255-258(2012).

[87] Economo M N, Clack N G, Lavis L D et al. A platform for brain-wide imaging and reconstruction of individual neurons[J]. eLife, 5, e10566(2016).

[88] Abdeladim L, Matho K S, Clavreul S et al. Multicolor multiscale brain imaging with chromatic multiphoton serial microscopy[J]. Nature Communications, 10, 1662(2019).

[89] Kim Y, Venkataraju K U, Pradhan K et al. Mapping social behavior-induced brain activation at cellular resolution in the mouse[J]. Cell Reports, 10, 292-305(2015).

[90] Vousden D A, Epp J, Okuno H et al. Whole-brain mapping of behaviourally induced neural activation in mice[J]. Brain Structure and Function, 220, 2043-2057(2015).

[91] Seiriki K, Kasai A, Hashimoto T et al. High-speed and scalable whole-brain imaging in rodents and primates[J]. Neuron, 94, 1085-1100(2017).

[92] Seiriki K, Kasai A, Nakazawa T et al. Whole-brain block-face serial microscopy tomography at subcellular resolution using FAST[J]. Nature Protocols, 14, 1509-1529(2019).

[93] Chen H, Huang T Y, Yang Y X et al. Sparse imaging and reconstruction tomography for high-speed high-resolution whole-brain imaging[J]. Cell Reports Methods, 1, 100089(2021).

[94] Li A A, Gong H, Zhang B et al. Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain[J]. Science, 330, 1404-1408(2010).

[95] Yuan J, Gong H, Li A A et al. Visible rodent brain-wide networks at single-neuron resolution[J]. Frontiers in Neuroanatomy, 9, 70(2015).

[96] Gong H, Zeng S Q, Yan C et al. Continuously tracing brain-wide long-distance axonal projections in mice at a one-micron voxel resolution[J]. NeuroImage, 74, 87-98(2013).

[97] Zheng T, Yang Z Q, Li A A et al. Visualization of brain circuits using two-photon fluorescence micro-optical sectioning tomography[J]. Optics Express, 21, 9839-9850(2013).

[98] Gong H, Xu D L, Yuan J et al. High-throughput dual-colour precision imaging for brain-wide connectome with cytoarchitectonic landmarks at the cellular level[J]. Nature Communications, 7, 12142(2016).

[99] Xu D L, Jiang T, Li A A et al. Fast optical sectioning obtained by structured illumination microscopy using a digital mirror device[J]. Journal of Biomedical Optics, 18, 060503(2013).

[100] Jiang T, Long B, Gong H et al. A platform for efficient identification of molecular phenotypes of brain-wide neural circuits[J]. Scientific Reports, 7, 13891(2017).

[101] Luo Y L, Wang A L, Liu M M et al. Label-free brainwide visualization of senile plaque using cryo-micro-optical sectioning tomography[J]. Optics Letters, 42, 4247-4250(2017).

[102] Chen X, Zhang X Y, Zhong Q Y et al. Simultaneous acquisition of neuronal morphology and cytoarchitecture in the same Golgi-stained brain[J]. Biomedical Optics Express, 9, 230-244(2017).

[103] Yang X, Zhang Q, Huang F et al. High-throughput light sheet tomography platform for automated fast imaging of whole mouse brain[J]. Journal of Biophotonics, 11, 201800047(2018).

[104] Zhang X Y, Chen Y F, Ning K F et al. Deep learning optical-sectioning method[J]. Optics Express, 26, 30762-30772(2018).

[105] Ning K F, Zhang X Y, Gao X F et al. Deep-learning-based whole-brain imaging at single-neuron resolution[J]. Biomedical Optics Express, 11, 3567-3584(2020).

[106] Wang X J, Xiong H Q, Liu Y R et al. Chemical sectioning fluorescence tomography: high-throughput, high-contrast, multicolor, whole-brain imaging at subcellular resolution[J]. Cell Reports, 34, 108709(2021).

[107] Xiong H Q, Zhou Z Q, Zhu M Q et al. Chemical reactivation of quenched fluorescent protein molecules enables resin-embedded fluorescence microimaging[J]. Nature Communications, 5, 3992(2014).

[108] Zhong Q Y, Li A A, Jin R et al. High-definition imaging using line-illumination modulation microscopy[J]. Nature Methods, 18, 309-315(2021).

[109] Zhou C, Yang X Q, Wu S H et al. Continuous subcellular resolution three-dimensional imaging on intact macaque brain[J]. Science Bulletin, 67, 85-96(2022).

[110] Deng L, Chen J W, Li Y F et al. Cryo-fluorescence micro-optical sectioning tomography for volumetric imaging of various whole organs with subcellular resolution[J]. iScience, 25, 104805(2022).

[111] Qiu L Y, Zhang B, Gao Z H. Lighting up neural circuits by viral tracing[J]. Neuroscience Bulletin, 1-14(2022).

[112] Liu Q, Wu Y, Wang H D et al. Viral tools for neural circuit tracing[J]. Neuroscience Bulletin, 1-11(2022).

[113] Frégnac Y. Big data and the industrialization of neuroscience: a safe roadmap for understanding the brain?[J]. Science, 358, 470-477(2017).

[114] Li A A, Guan Y, Gong H et al. Challenges of processing and analyzing big data in mesoscopic whole-brain imaging[J]. Genomics, Proteomics & Bioinformatics, 17, 337-343(2019).

[115] Li S W, Quan T W, Zhou H et al. Review of advances and prospects in neuron reconstruction[J]. Chinese Science Bulletin, 64, 532-545(2019).

[116] Bjerke I E, Øvsthus M, Papp E A et al. Data integration through brain atlasing: human brain project tools and strategies[J]. European Psychiatry, 50, 70-76(2018).

[117] Huang Z J, Luo L Q. It takes the world to understand the brain[J]. Science, 350, 42-44(2015).

[118] Okano H, Miyawaki A, Kasai K. Brain/MINDS: brain-mapping project in Japan[J]. Philosophical Transactions of the Royal Society B: Biological Sciences, 370, 20140310(2015).

[119] Herculano-Houzel S. The human brain in numbers: a linearly scaled-up primate brain[J]. Frontiers in Human Neuroscience, 3, 31(2009).