Deep tissue two-photon microscopy

Resting microglial cells are highly dynamic surveillants of brain parenchyma in vivo

Nimmerjahn, A., Kirchhoff, F., & Helmchen, F. (2005) · Science · doi:10.1126/science.1110647 · Cited by 5,827

ATP mediates rapid microglial response to local brain injury in vivo

Davalos, D., Grutzendler, J., Yang, G., Kim, J. V., Zuo, Y., Jung, S., Littman, D. R., Dustin, M. L., & Gan, W.-B. (2005) · Nature Neuroscience · doi:10.1038/nn1472 · Cited by 3,913

Long-term in vivo imaging of experience-dependent synaptic plasticity in adult cortex

Trachtenberg, J. T., Chen, B. E., Knott, G. W., Feng, G., Sanes, J. R., Welker, E., & Svoboda, K. (2002) · Nature · doi:10.1038/nature01273 · Cited by 1,927

Dendritic spine geometry is critical for AMPA receptor expression in hippocampal CA1 pyramidal neurons

Matsuzaki, M., Ellis-Davies, G. C. R., Nemoto, T., Miyashita, Y., Iino, M., & Kasai, H. (2001) · Nature Neuroscience · doi:10.1038/nn736 · Cited by 1,563

Second-harmonic imaging microscopy for visualizing biomolecular arrays in cells, tissues and organisms

Campagnola, P. J., & Loew, L. M. (2003) · Nature Biotechnology · doi:10.1038/nbt894 · Cited by 1,326

Long-term dendritic spine stability in the adult cortex

Grutzendler, J., Kasthuri, N., & Gan, W.-B. (2002) · Nature · doi:10.1038/nature01276 · Cited by 1,198 · cited 1×

Fluctuations and stimulus-induced changes in blood flow observed in individual capillaries in layers 2 through 4 of rat neocortex

Kleinfeld, D., Mitra, P. P., Helmchen, F., & Denk, W. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.26.15741 · Cited by 832

Experience-dependent plasticity of dendritic spines in the developing rat barrel cortex in vivo

Lendvai, B., Stern, E. A., Chen, B., & Svoboda, K. (2000) · Nature · doi:10.1038/35009107 · Cited by 802

Sulforhodamine 101 as a specific marker of astroglia in the neocortex in vivo

Nimmerjahn, A., Kirchhoff, F., Kerr, J. N. D., & Helmchen, F. (2004) · Nature Methods · doi:10.1038/nmeth706 · Cited by 784

Fibrillar amyloid deposition leads to local synaptic abnormalities and breakage of neuronal branches

Tsai, J., Grutzendler, J., Duff, K., & Gan, W.-B. (2004) · Nature Neuroscience · doi:10.1038/nn1335 · Cited by 561

Aggregation-Induced Emission: Together We Shine, United We Soar!

Mei, J., Leung, N. L. C., Kwok, R. T. K., Lam, J. W. Y., & Tang, B. Z. (2015) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00263 · Cited by 8,270

Aggregation‐Induced Emission: The Whole Is More Brilliant than the Parts

Mei, J., Hong, Y., Lam, J. W. Y., Qin, A., Tang, Y., & Tang, B. Z. (2014) · Advanced Materials · doi:10.1002/adma.201401356 · Cited by 3,381

The Fluorescent Toolbox for Assessing Protein Location and Function

Giepmans, B. N. G., Adams, S. R., Ellisman, M. H., & Tsien, R. Y. (2006) · Science · doi:10.1126/science.1124618 · Cited by 2,770

Structural and molecular interrogation of intact biological systems

Chung, K., Wallace, J., Kim, S.-Y., Kalyanasundaram, S., Andalman, A. S., Davidson, T. J., Mirzabekov, J. J., Zalocusky, K. A., Mattis, J., Denisin, A. K., et al. (2013) · Nature · doi:10.1038/nature12107 · Cited by 2,008

Experience-dependent structural synaptic plasticity in the mammalian brain

Holtmaat, A., & Svoboda, K. (2009) · Nature Reviews Neuroscience · doi:10.1038/nrn2699 · Cited by 1,934

Going deeper than microscopy: the optical imaging frontier in biology

Ntziachristos, V. (2010) · Nature Methods · doi:10.1038/nmeth.1483 · Cited by 1,896

Controlling waves in space and time for imaging and focusing in complex media

Mosk, A. P., Lagendijk, A., Lerosey, G., & Fink, M. (2012) · Nature Photonics · doi:10.1038/nphoton.2012.88 · Cited by 1,536

In vivo three-photon microscopy of subcortical structures within an intact mouse brain

Horton, N. G., Wang, K., Kobat, D., Clark, C. G., Wise, F. W., Schaffer, C. B., & Xu, C. (2013) · Nature Photonics · doi:10.1038/nphoton.2012.336 · Cited by 1,505

Real-time imaging reveals the single steps of brain metastasis formation.

Kienast, Y., von Baumgarten, L., Fuhrmann, M., Klinkert, W. E. F., Goldbrunner, R., Herms, J., & Winkler, F. (2010) · Nature Medicine · doi:10.1038/nm.2072 · Cited by 1,138

Small-Molecule Two-Photon Probes for Bioimaging Applications

Kim, H. M., & Cho, B. R. (2015) · Chemical Reviews · doi:10.1021/cr5004425 · Cited by 1,047

Principles of two-photon excitation microscopy and its applications to neuroscience

Svoboda, K., & Yasuda, R. (2006) · Neuron · doi:10.1016/j.neuron.2006.05.019 · Cited by 1,027

Advanced CLARITY for rapid and high-resolution imaging of intact tissues

Tomer, R., Ye, L., Hsueh, B., & Deisseroth, K. (2014) · Nature Protocols · doi:10.1038/nprot.2014.123 · Cited by 842

CLARITY for mapping the nervous system

Chung, K., & Deisseroth, K. (2013) · Nature Methods · doi:10.1038/nmeth.2481 · Cited by 747

Selective plane illumination microscopy techniques in developmental biology

Huisken, J., & Stainier, D. Y. R. (2009) · Development · doi:10.1242/dev.022426 · Cited by 608

Carbon-based nanomaterials as an emerging platform for theranostics

Patel, K. D., Singh, R. K., & Kim, H.-W. (2019) · Materials Horizons · doi:10.1039/c8mh00966j · Cited by 555

Sympathetic Neuro-adipose Connections Mediate Leptin-Driven Lipolysis

Zeng, W., Pirzgalska, R. M., Pereira, M. M. A., Kubasova, N., Barateiro, A., Seixas, E., Lu, Y.-H., Kozlova, A., Voss, H., Martins, G. G., et al. (2015) · Cell · doi:10.1016/j.cell.2015.08.055 · Cited by 490

Central pathways of pulmonary and lower airway vagal afferents.

Kubin, L., Alheid, G. F., Zuperku, E. J., & McCrimmon, D. R. (2006) · Journal of Applied Physiology · doi:10.1152/japplphysiol.00252.2006 · Cited by 477

One-pot green synthesis of carbon dots by using Saccharum officinarum juice for fluorescent imaging of bacteria (Escherichia coli) and yeast (Saccharomyces cerevisiae) cells

Mehta, V. N., Jha, S., & Kailasa, S. K. (2014) · Materials Science and Engineering: C · doi:10.1016/j.msec.2014.01.038 · Cited by 441

Improving brightness and photostability of green and red fluorescent proteins for live cell imaging and FRET reporting

Bajar, B. T., Wang, E. S., Lam, A. J., Kim, B. B., Jacobs, C. L., Howe, E. S., Davidson, M. W., Lin, M. Z., & Chu, J. (2016) · Scientific Reports · doi:10.1038/srep20889 · Cited by 389

Subtissue Thermal Sensing Based on Neodymium-Doped LaF3Nanoparticles

Rocha, U., Jacinto da Silva, C., Ferreira Silva, W., Guedes, I., Benayas, A., Martínez Maestro, L., Acosta Elias, M., Bovero, E., van Veggel, F. C. J. M., García Solé, J. A., et al. (2013) · ACS Nano · doi:10.1021/nn304373q · Cited by 382

The Big and the Small: Challenges of Imaging the Brain’s Circuits

Lichtman, J. W., & Denk, W. (2011) · Science · doi:10.1126/science.1209168 · Cited by 370

Ratiometric Detection of Mitochondrial Thiols with a Two-Photon Fluorescent Probe

Lim, C. S., Masanta, G., Kim, H. J., Han, J. H., Kim, H. M., & Cho, B. R. (2011) · Journal of the American Chemical Society · doi:10.1021/ja205081s · Cited by 365

Barrel cortex function

Feldmeyer, D., Brecht, M., Helmchen, F., Petersen, C. C. H., Poulet, J. F. A., Staiger, J. F., Luhmann, H. J., & Schwarz, C. (2013) · Progress in Neurobiology · doi:10.1016/j.pneurobio.2012.11.002 · Cited by 354

Two-photon optogenetic toolbox for fast inhibition, excitation and bistable modulation

Prakash, R., Yizhar, O., Grewe, B., Ramakrishnan, C., Wang, N., Goshen, I., Packer, A. M., Peterka, D. S., Yuste, R., Schnitzer, M. J., et al. (2012) · Nature Methods · doi:10.1038/nmeth.2215 · Cited by 334

In Vivo Voltage-Sensitive Dye Imaging in Adult Mice Reveals That Somatosensory Maps Lost to Stroke Are Replaced over Weeks by New Structural and Functional Circuits with Prolonged Modes of Activation within Both the Peri-Infarct Zone and Distant Sites

Brown, C. E., Aminoltejari, K., Erb, H., Winship, I. R., & Murphy, T. H. (2009) · The Journal of Neuroscience · doi:10.1523/jneurosci.4249-08.2009 · Cited by 319

Optical Imaging Using Endogenous Contrast to Assess Metabolic State

Georgakoudi, I., & Quinn, K. P. (2012) · Annual Review of Biomedical Engineering · doi:10.1146/annurev-bioeng-071811-150108 · Cited by 316

Low-Contrast Dielectric Metasurface Optics

Zhan, A., Colburn, S., Trivedi, R., Fryett, T. K., Dodson, C. M., & Majumdar, A. (2016) · ACS Photonics · doi:10.1021/acsphotonics.5b00660 · Cited by 306

Dendritic spines: from structure to in vivo function

Rochefort, N. L., & Konnerth, A. (2012) · The EMBO Reports · doi:10.1038/embor.2012.102 · Cited by 299

Volume scanning electron microscopy for imaging biological ultrastructure

Titze, B., & Genoud, C. (2016) · Biology of the Cell · doi:10.1111/boc.201600024 · Cited by 287

Thiol Reactive Probes and Chemosensors

Peng, H., Chen, W., Cheng, Y., Hakuna, L., Strongin, R., & Wang, B. (2012) · Sensors · doi:10.3390/s121115907 · Cited by 275

Neuronal hyperactivity--A key defect in Alzheimer’s disease?

Busche, M. A., & Konnerth, A. (2015) · BioEssays · doi:10.1002/bies.201500004 · Cited by 266

Communication between neurons and astrocytes: relevance to the modulation of synaptic and network activity

Fellin, T. (2009) · Journal of Neurochemistry · doi:10.1111/j.1471-4159.2008.05830.x · Cited by 245

Two-photon excitation STED microscopy

Moneron, G., & Hell, S. W. (2009) · Optics Express · doi:10.1364/oe.17.014567 · Cited by 238

Light-sheet microscopy in the near-infrared II window

Wang, F., Wan, H., Ma, Z., Zhong, Y., Sun, Q., Tian, Y., Qu, L., Du, H., Zhang, M., Li, L., et al. (2019) · Nature Methods · doi:10.1038/s41592-019-0398-7 · Cited by 237

Aggregation-Induced Emission Luminogen with Near-Infrared-II Excitation and Near-Infrared-I Emission for Ultradeep Intravital Two-Photon Microscopy

Qi, J., Sun, C., Li, D., Zhang, H., Yu, W., Zebibula, A., Lam, J. W. Y., Xi, W., Zhu, L., Cai, F., et al. (2018) · ACS Nano · doi:10.1021/acsnano.8b02452 · Cited by 226

In vivo two-photon microscopy reveals immediate microglial reaction to implantation of microelectrode through extension of processes

Kozai, T. D. Y., Vazquez, A. L., Weaver, C. L., Kim, S.-G., & Cui, X. T. (2012) · Journal of Neural Engineering · doi:10.1088/1741-2560/9/6/066001 · Cited by 215

Genetically encoded optical indicators for the analysis of neuronal circuits

Knöpfel, T. (2012) · Nature reviews. Neuroscience · doi:10.1038/nrn3293 · Cited by 205

Multicellular tumor spheroids as an in vivo-like tumor model for three-dimensional imaging of chemotherapeutic and nano material cellular penetration

Ma, H.-L., Jiang, Q., Han, S., Wu, Y., Tomshine, J. C., Wang, D., Gan, Y., Zou, G., & Liang, X.-J. (2012) · Molecular Imaging · doi:10.2310/7290.2012.00012 · Cited by 182

Aggregation-Induced Emission Luminogen with Deep-Red Emission for Through-Skull Three-Photon Fluorescence Imaging of Mouse

Wang, Y., Chen, M., Alifu, N., Li, S., Qin, W., Qin, A., Tang, B. Z., & Qian, J. (2017) · ACS Nano · doi:10.1021/acsnano.7b05645 · Cited by 177

Two distinct layer-specific dynamics of cortical ensembles during learning of a motor task

Masamizu, Y., Tanaka, Y. R., Tanaka, Y. H., Hira, R., Ohkubo, F., Kitamura, K., Isomura, Y., Okada, T., & Matsuzaki, M. (2014) · Nature Neuroscience · doi:10.1038/nn.3739 · Cited by 164

Multimodal modeling of neural network activity: computing LFP, ECoG, EEG, and MEG signals with LFPy 2.0

Hagen, E., Næss, S., Ness, T. V., & Einevoll, G. T. (2018) · Frontiers in Neuroinformatics · doi:10.3389/fninf.2018.00092 · Cited by 129

Recent Advances in Electrical Neural Interface Engineering: Minimal Invasiveness, Longevity, and Scalability

Luan, L., Robinson, J. T., Aazhang, B., Chi, T., Yang, K., Li, X., Rathore, H., Singer, A., Yellapantula, S., Fan, Y., et al. (2020) · Neuron · doi:10.1016/j.neuron.2020.10.011 · Cited by 150

Dynamic Analyses of Drosophila Gastrulation Provide Insights into Collective Cell Migration

McMahon, A., Supatto, W., Fraser, S. E., & Stathopoulos, A. (2008) · Science · doi:10.1126/science.1167094 · Cited by 148

NIR‐II‐Excited Intravital Two‐Photon Microscopy Distinguishes Deep Cerebral and Tumor Vasculatures with an Ultrabright NIR‐I AIE Luminogen

Wang, S., Liu, J., Goh, C. C., Ng, L. G., & Liu, B. (2019) · Advanced Materials · doi:10.1002/adma.201904447 · Cited by 148

Deep learning for in vivo near-infrared imaging

Ma, Z., Wang, F., Wang, W., Zhong, Y., & Dai, H. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2021446118 · Cited by 135

Calcium imaging of sleep-wake related neuronal activity in the dorsal pons

Cox, J., Pinto, L., & Dan, Y. (2016) · Nature Communications · doi:10.1038/ncomms10763 · Cited by 133

Nanoscopy of living brain slices with low light levels

Testa, I., Urban, N. T., Jakobs, S., Eggeling, C., Willig, K. I., & Hell, S. W. (2012) · Neuron · doi:10.1016/j.neuron.2012.07.028 · Cited by 131

Functional tomographic fluorescence imaging of pH microenvironments in microbial biofilms by use of silica nanoparticle sensors

Hidalgo, G., Burns, A., Herz, E., Hay, A. G., Houston, P. L., Wiesner, U., & Lion, L. W. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.01220-09 · Cited by 127

Where are we? The anatomy of the murine cortical meninges revisited for intravital imaging, immunology, and clearance of waste from the brain

Coles, J. A., Myburgh, E., Brewer, J. M., & McMenamin, P. G. (2017) · Progress in Neurobiology · doi:10.1016/j.pneurobio.2017.05.002 · Cited by 123

NIR‐II Excitable Conjugated Polymer Dots with Bright NIR‐I Emission for Deep In Vivo Two‐Photon Brain Imaging Through Intact Skull

Wang, S., Liu, J., Feng, G., Ng, L. G., & Liu, B. (2019) · Advanced Functional Materials · doi:10.1002/adfm.201808365 · Cited by 110

NIR‐II Light Activated Photosensitizer with Aggregation‐Induced Emission for Precise and Efficient Two‐Photon Photodynamic Cancer Cell Ablation

Wang, S., Chen, H., Liu, J., Chen, C., & Liu, B. (2020) · Advanced Functional Materials · doi:10.1002/adfm.202002546 · Cited by 103

Shedding new light on lipid functions with CARS and SRS microscopy

Yu, Y., Ramachandran, P. V., & Wang, M. C. (2014) · Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids · doi:10.1016/j.bbalip.2014.02.003 · Cited by 89

Two-Photon Absorption: An Open Door to the NIR-II Biological Window?

Shaw, P. A., Forsyth, E., Haseeb, F., Yang, S., Bradley, M., & Klausen, M. (2022) · Frontiers in Chemistry · doi:10.3389/fchem.2022.921354 · Cited by 75

Six-color intravital two-photon imaging of brain tumors and their dynamic microenvironment

Ricard, C., & Debarbieux, F. C. (2014) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2014.00057 · Cited by 75

Imaging neuromodulators with high spatiotemporal resolution using genetically encoded indicators

Patriarchi, T., Cho, J. R., Merten, K., Marley, A., Broussard, G. J., Liang, R., Williams, J., Nimmerjahn, A., von Zastrow, M., Gradinaru, V., et al. (2019) · Nature Protocols · doi:10.1038/s41596-019-0239-2 · Cited by 66

Rapid, reproducible transduction of select forebrain regions by targeted recombinant virus injection into the neonatal mouse brain

Pilpel, N., Landeck, N., Klugmann, M., Seeburg, P. H., & Schwarz, M. K. (2009) · Journal of Neuroscience Methods · doi:10.1016/j.jneumeth.2009.05.020 · Cited by 61

Cyclosporine-loaded micelles for ocular delivery: investigating the penetration mechanisms

Ghezzi, M., Ferraboschi, I., Delledonne, A., Pescina, S., Padula, C., Santi, P., Sissa, C., Terenziani, F., & Nicoli, S. (2022) · Journal of Controlled Release · doi:10.1016/j.jconrel.2022.07.019 · Cited by 63

Fluorescence Lifetime Imaging Microscopy for Quantitative Biological Imaging

Chen, L.-C., Lloyd, W. R., Chang, C.-W., Sud, D., & Mycek, M.-A. (2013) · Methods in Cell Biology · doi:10.1016/b978-0-12-407761-4.00020-8 · Cited by 55

Two-Photon Imaging of Microglia in the Mouse Cortex In Vivo

Nimmerjahn, A. (2012) · Cold Spring Harbor Protocols · doi:10.1101/pdb.prot069294 · Cited by 38

Molecular neuroanatomy: a generation of progress

Pollock, J. D., Wu, D.-Y., & Satterlee, J. S. (2014) · Trends in Neurosciences · doi:10.1016/j.tins.2013.11.001 · Cited by 36

Tunneling nanotubes: The transport highway for astrocyte-neuron communication in the central nervous system

Zhou, C., Huang, M., Wang, S., Chu, S., Zhang, Z., & Chen, N. (2024) · Brain Research Bulletin · doi:10.1016/j.brainresbull.2024.110921 · Cited by 34

Fungal Infection in the Brain: What We Learned from Intravital Imaging

Shi, M., & Mody, C. H. (2016) · Frontiers in Immunology · doi:10.3389/fimmu.2016.00292 · Cited by 33

Real-time in vivo imaging of fungal migration to the central nervous system: Visualizing fungal migration to the CNS

Shi, M., Calaruso, P., & Mody, C. H. (2012) · Cellular Microbiology · doi:10.1111/cmi.12027 · Cited by 32

Fluorescence imaging of synapse formation and remodeling

Okabe, S. (2013) · Microscopy · doi:10.1093/jmicro/dfs083 · Cited by 26

Adaptive Optical Two-Photon Microscopy for Surface-Profiled Living Biological Specimens

Yamaguchi, K., Otomo, K., Kozawa, Y., Tsutsumi, M., Inose, T., Hirai, K., Sato, S., Nemoto, T., & Uji-i, H. (2021) · ACS Omega · doi:10.1021/acsomega.0c04888 · Cited by 19

Validation and tuning of in situ transcriptomics image processing workflows with crowdsourced annotations

Vo-Phamhi, J. M., Yamauchi, K. A., & Gómez-Sjöberg, R. (2021) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1009274 · Cited by 1