The DOI matches its Crossref record; 44 of the 44 references it cites were found in a registry or an index.
Super-Resolution Mapping of Neuronal Circuitry With an Index-Optimized Clearing Agent
Open accessAbstract
Super-resolution imaging deep inside tissues has been challenging, as it is extremely sensitive to light scattering and spherical aberrations. Here, we report an optimized optical clearing agent for high-resolution fluorescence imaging (SeeDB2). SeeDB2 matches the refractive indices of fixed tissues to that of immersion oil (1.518), thus minimizing both light scattering and spherical aberrations. During the clearing process, fine morphology and fluorescent proteins were highly preserved. SeeDB2 enabled super-resolution microscopy of various tissue samples up to a depth of >100 μm, an order of magnitude deeper than previously possible under standard mounting conditions. Using this approach, we demonstrate accumulation of inhibitory synapses on spine heads in NMDA-receptor-deficient neurons. In the fly medulla, we found unexpected heterogeneity in axon bouton orientations among Mi1 neurons, a part of the motion detection circuitry. Thus, volumetric super-resolution microscopy of cleared tissues is a powerful strategy in connectomic studies at synaptic levels.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Imaging Neuronal Subsets in Transgenic Mice Expressing Multiple Spectral Variants of GFP
Feng, G., Mellor, R. H., Bernstein, M., Keller-Peck, C., Nguyen, Q. T., Wallace, M., Nerbonne, J. M., Lichtman, J. W., & Sanes, J. R. (2000) · Neuron · doi:10.1016/s0896-6273(00)00084-2 · Cited by 3,042
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
Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution
Chen, B.-C., Legant, W. R., Wang, K., Shao, L., Milkie, D. E., Davidson, M. W., Janetopoulos, C., Wu, X. S., Hammer, J. A., Liu, Z., et al. (2014) · Science · doi:10.1126/science.1257998 · Cited by 1,919
Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system
Livet, J., Weissman, T. A., Kang, H., Draft, R. W., Lu, J., Bennis, R. A., Sanes, J. R., & Lichtman, J. W. (2007) · Nature · doi:10.1038/nature06293 · Cited by 1,876
Chen, F., Tillberg, P. W., & Boyden, E. S. (2015) · Science · doi:10.1126/science.1260088 · Cited by 1,501
Whole-Brain Imaging with Single-Cell Resolution Using Chemical Cocktails and Computational Analysis
Susaki, E. A., Tainaka, K., Perrin, D., Kishino, F., Tawara, T., Watanabe, T. M., Yokoyama, C., Onoe, H., Eguchi, M., Yamaguchi, S., et al. (2014) · Cell · doi:10.1016/j.cell.2014.03.042 · Cited by 1,325
Subregion- and Cell Type–Restricted Gene Knockout in Mouse Brain
Tsien, J. Z., Chen, D. F., Gerber, D., Tom, C., Mercer, E. H., Anderson, D. J., Mayford, M., Kandel, E. R., & Tonegawa, S. (1996) · Cell · doi:10.1016/s0092-8674(00)81826-7 · Cited by 1,280
A guide to super-resolution fluorescence microscopy
Schermelleh, L., Heintzmann, R., & Leonhardt, H. (2010) · Journal of Cell Biology · doi:10.1083/jcb.201002018 · Cited by 1,255
Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain
Hama, H., Kurokawa, H., Kawano, H., Ando, R., Shimogori, T., Noda, H., Fukami, K., Sakaue-Sawano, A., & Miyawaki, A. (2011) · Nature Neuroscience · doi:10.1038/nn.2928 · Cited by 1,142
Richardson, D. S., & Lichtman, J. W. (2015) · Cell · doi:10.1016/j.cell.2015.06.067 · Cited by 1,095
Saturated Reconstruction of a Volume of Neocortex
Kasthuri, N., Hayworth, K. J., Berger, D. R., Schalek, R. L., Conchello, J. A., Knowles-Barley, S., Lee, D., Vázquez-Reina, A., Kaynig, V., Jones, T. R., et al. (2015) · Cell · doi:10.1016/j.cell.2015.06.054 · Cited by 1,044
Single-Cell Phenotyping within Transparent Intact Tissue through Whole-Body Clearing
Yang, B., Treweek, J. B., Kulkarni, R. P., Deverman, B. E., Chen, C.-K., Lubeck, E., Shah, S., Cai, L., & Gradinaru, V. (2014) · Cell · doi:10.1016/j.cell.2014.07.017 · Cited by 925
SeeDB: a simple and morphology-preserving optical clearing agent for neuronal circuit reconstruction
Ke, M.-T., Fujimoto, S., & Imai, T. (2013) · Nature Neuroscience · doi:10.1038/nn.3447 · Cited by 892
Self-citationAdvanced 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
Micheva, K. D., & Smith, S. J. (2007) · Neuron · doi:10.1016/j.neuron.2007.06.014 · Cited by 787
Superresolution Imaging of Chemical Synapses in the Brain
Dani, A., Huang, B., Bergan, J., Dulac, C., & Zhuang, X. (2010) · Neuron · doi:10.1016/j.neuron.2010.11.021 · Cited by 725
A visual motion detection circuit suggested by Drosophila connectomics
Takemura, S.-Y., Bharioke, A., Lu, Z., Nern, A., Vitaladevuni, S., Rivlin, P. K., Katz, W. T., Olbris, D. J., Plaza, S. M., Winston, P., et al. (2013) · Nature · doi:10.1038/nature12450 · Cited by 686
Aberrations in confocal fluorescence microscopy induced by mismatches in refractive index
HELL, S., REINER, G., CREMER, C., & STELZER, E. H. K. (1993) · Journal of Microscopy · doi:10.1111/j.1365-2818.1993.tb03315.x · Cited by 640
ScaleS: an optical clearing palette for biological imaging
Hama, H., Hioki, H., Namiki, K., Hoshida, T., Kurokawa, H., Ishidate, F., Kaneko, T., Akagi, T., Saito, T., Saido, T., et al. (2015) · Nature Neuroscience · doi:10.1038/nn.4107 · Cited by 603
Spine neck plasticity regulates compartmentalization of synapses
Tønnesen, J., Katona, G., Rózsa, B., & Nägerl, U. V. (2014) · Nature Neuroscience · doi:10.1038/nn.3682 · Cited by 444
Huff, J. (2015) · Nature Methods · doi:10.1038/nmeth.f.388 · Cited by 426
A directional tuning map of Drosophila elementary motion detectors
Maisak, M. S., Haag, J., Ammer, G., Serbe, E., Meier, M., Leonhardt, A., Schilling, T., Bahl, A., Rubin, G. M., Nern, A., et al. (2013) · Nature · doi:10.1038/nature12320 · Cited by 390
Live-cell 3D super-resolution imaging in thick biological samples
Cella Zanacchi, F., Lavagnino, Z., Perrone Donnorso, M., Del Bue, A., Furia, L., Faretta, M., & Diaspro, A. (2011) · Nature Methods · doi:10.1038/nmeth.1744 · Cited by 385
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
Clustered dynamics of inhibitory synapses and dendritic spines in the adult neocortex.
Chen, J. L., Villa, K. L., Cha, J. W., So, P. T. C., Kubota, Y., & Nedivi, E. (2012) · Neuron · doi:10.1016/j.neuron.2012.02.030 · Cited by 341
Odorant ReceptorDerived cAMP Signals Direct Axonal Targeting
Imai, T., Suzuki, M., & Sakano, H. (2006) · Science · doi:10.1126/science.1131794 · Cited by 329
Self-citationKitajima, T. S., Ohsugi, M., & Ellenberg, J. (2011) · Cell · doi:10.1016/j.cell.2011.07.031 · Cited by 299
Self-citationSTED Nanoscopy of Actin Dynamics in Synapses Deep Inside Living Brain Slices
Urban, N. T., Willig, K. I., Hell, S. W., & Nägerl, U. V. (2011) · Biophysical Journal · doi:10.1016/j.bpj.2011.07.027 · Cited by 297
2,2′‐Thiodiethanol: A new water soluble mounting medium for high resolution optical microscopy
Staudt, T., Lang, M. C., Medda, R., Engelhardt, J., & Hell, S. W. (2007) · Microscopy Research and Technique · doi:10.1002/jemt.20396 · Cited by 291
Establishment of conditional reporter mouse lines at ROSA26 locus for live cell imaging
Abe, T., Kiyonari, H., Shioi, G., Inoue, K., Nakao, K., Aizawa, S., & Fujimori, T. (2011) · genesis · doi:10.1002/dvg.20753 · Cited by 249
Two-photon excitation STED microscopy
Moneron, G., & Hell, S. W. (2009) · Optics Express · doi:10.1364/oe.17.014567 · Cited by 238
BigNeuron: Large-Scale 3D Neuron Reconstruction from Optical Microscopy Images
Peng, H., Hawrylycz, M., Roskams, J., Hill, S., Spruston, N., Meijering, E., & Ascoli, G. A. (2015) · Neuron · doi:10.1016/j.neuron.2015.06.036 · Cited by 232
Common circuit design in fly and mammalian motion vision
Borst, A., & Helmstaedter, M. (2015) · Nature Neuroscience · doi:10.1038/nn.4050 · Cited by 220
Regulation of spine morphology and spine density by NMDA receptor signaling in vivo
Ultanir, S. K., Kim, J.-E., Hall, B. J., Deerinck, T., Ellisman, M., & Ghosh, A. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0704031104 · Cited by 187
Ding, J. B., Takasaki, K. T., & Sabatini, B. L. (2009) · Neuron · doi:10.1016/j.neuron.2009.07.011 · Cited by 177
Large-Scale Automated Histology in the Pursuit of Connectomes
Kleinfeld, D., Bharioke, A., Blinder, P., Bock, D. D., Briggman, K. L., Chklovskii, D. B., Denk, W. T., Helmstaedter, M. N., Kaufhold, J. P., Lee, W.-C. A., et al. (2011) · Journal of Neuroscience · doi:10.1523/jneurosci.4077-11.2011 · Cited by 161
Mapping Synaptic Input Fields of Neurons with Super-Resolution Imaging
Sigal, Y. M., Speer, C. M., Babcock, H. P., & Zhuang, X. (2015) · Cell · doi:10.1016/j.cell.2015.08.033 · Cited by 126
Concentric zones, cell migration and neuronal circuits in the Drosophila visual center
Hasegawa, E., Kitada, Y., Kaido, M., Takayama, R., Awasaki, T., Tabata, T., & Sato, M. (2011) · Development · doi:10.1242/dev.058370 · Cited by 124
Self-citationCandidate Neural Substrates for Off-Edge Motion Detection in Drosophila
Shinomiya, K., Karuppudurai, T., Lin, T., Lu, Z., Lee, C., & Meinertzhagen, I. A. (2014) · Current Biology · doi:10.1016/j.cub.2014.03.051 · Cited by 116
Ultrafast superresolution fluorescence imaging with spinning disk confocal microscope optics
Hayashi, S., & Okada, Y. (2015) · Molecular Biology of the Cell · doi:10.1091/mbc.e14-08-1287 · Cited by 106
Superresolution imaging for neuroscience
Tønnesen, J., & Nägerl, U. V. (2012) · Experimental Neurology · doi:10.1016/j.expneurol.2012.10.004 · Cited by 90
Optical super-resolution microscopy in neurobiology
Sigrist, S. J., & Sabatini, B. L. (2011) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2011.10.014 · Cited by 58
Optical Clearing of Fixed Brain Samples Using SeeDB
Ke, M., & Imai, T. (2014) · Current Protocols in Neuroscience · doi:10.1002/0471142301.ns0222s66 · Cited by 57
Self-citationBaho, E., & Cristo, G. D. (2012) · Journal of Neuroscience · doi:10.1523/jneurosci.4352-11.2012 · Cited by 32
Cited by
STED super-resolved microscopy
Vicidomini, G., Bianchini, P., & Diaspro, A. (2018) · Nature Methods · doi:10.1038/nmeth.4593 · Cited by 717
Protection of tissue physicochemical properties using polyfunctional crosslinkers
Park, Y.-G., Sohn, C. H., Chen, R., McCue, M., Yun, D. H., Drummond, G. T., Ku, T., Evans, N. B., Oak, H. C., Trieu, W., et al. (2019) · Nature Biotechnology · doi:10.1038/nbt.4281 · Cited by 421
Murakami, T. C., Mano, T., Saikawa, S., Horiguchi, S. A., Shigeta, D., Baba, K., Sekiya, H., Shimizu, Y., Tanaka, K. F., Kiyonari, H., et al. (2018) · Nature Neuroscience · doi:10.1038/s41593-018-0109-1 · Cited by 292
Nishiyama, J., Mikuni, T., & Yasuda, R. (2017) · Neuron · doi:10.1016/j.neuron.2017.10.004 · Cited by 215
A guidebook for DISCO tissue clearing
Molbay, M., Kolabas, Z. I., Todorov, M. I., Ohn, T., & Ertürk, A. (2021) · Molecular Systems Biology · doi:10.15252/msb.20209807 · Cited by 96
Metadata
- Authors
- Ke, M.-T., Nakai, Y., Fujimoto, S., Takayama, R., Yoshida, S., Kitajima, T. S., Sato, M., & Imai, T.
- Venue
- Cell Reports
- Publisher
- Elsevier BV
- Published
- 2016-03
- Volume
- 14
- Issue
- 11
- Pages
- 2718-2732
- ISSN
- 2211-1247 (ISSN-L)
- OpenAlex
- W2296740725
- Cited by
- 264
- References
- 44
- FWCI
- 18.41
- Type
- journal article
- Language
- en
- Open access
- gold
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.