Dunn, R. C. Near-field scanning optical microscopy. Chem. Rev. 99, 2891–2928 (1999).
Dürig, U., Pohl, D. W. & Rohner, F. Near-field optical-scanning microscopy. J. Appl. Phys. 59, 3318–3327 (1986).
Hell, S.W. Far-field optical nanoscopy. In Proc. 2010 23rd Annual Meeting of the IEEE Photonics Society (eds Jagadish, C. et al.) 3–4 (IEEE, New York, 2010).
Huang, B., Bates, M. & Zhuang, X. Super-resolution fluorescence microscopy. Annu. Rev. Biochem. 78, 993–1016 (2009).
Chen, F., Tillberg, P. W. & Boyden, E. S. Expansion microscopy. Science 347, 543–548 (2015).
Tanaka, T. et al. Phase transitions in ionic gels. Phys. Rev. Lett. 45, 1636–1639 (1980).
Hausen, P. & Dreyer, C. The use of polyacrylamide as an embedding medium for immunohistochemical studies of embryonic tissues. Stain Technol. 56, 287–293 (1981).
Cohen, Y., Ramon, O., Kopelman, I. J. & Mizrahi, S. Characterization of inhomogeneous polyacrylamide hydrogels. J. Polym. Sci. B Polym. Phys. 30, 1055–1067 (1992).
Tillberg, P. W. et al. Protein-retention expansion microscopy of cells and tissues labeled using standard fluorescent proteins and antibodies. Nat. Biotechnol. 34, 987–992 (2016).
Chen, F. et al. Nanoscale imaging of RNA with expansion microscopy. Nat. Methods 13, 679–684 (2016).
Chang, J.-B. et al. Iterative expansion microscopy. Nat. Methods 14, 593–599 (2017).
Zhao, Y. et al. Nanoscale imaging of clinical specimens using pathology-optimized expansion microscopy. Nat. Biotechnol. 35, 757–764 (2017).
Chozinski, T. J. et al. Expansion microscopy with conventional antibodies and fluorescent proteins. Nat. Methods 13, 485–488 (2016).
Ku, T. et al. Multiplexed and scalable super-resolution imaging of three-dimensional protein localization in size-adjustable tissues. Nat. Biotechnol. 34, 973–981 (2016).
Truckenbrodt, S. et al. X10 expansion microscopy enables 25-nm resolution on conventional microscopes. EMBO Rep. 19, e45836 (2018).
Tsanov, N. et al. smiFISH and FISH-quant—a flexible single RNA detection approach with super-resolution capability. Nucleic Acids Res. 44, e165 (2016).
Asano, S. M. et al. Expansion microscopy: protocols for imaging proteins and RNA in cells and tissues. Curr. Protoc. Cell Biol. 80, e56 (2018).
Freifeld, L. et al. Expansion microscopy of zebrafish for neuroscience and developmental biology studies. Proc. Natl Acad. Sci. USA 114, E10799–E10808 (2017).
Migliori, B. et al. Light sheet theta microscopy for rapid high-resolution imaging of large biological samples. BMC Biol. 16, 57 (2018).
Hama, H. et al. Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain. Nat. Neurosci. 14, 1481–1488 (2011).
Susaki, E. A. et al. Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis. Cell 157, 726–739 (2014).
Chung, K. et al. Structural and molecular interrogation of intact biological systems. Nature 497, 332–337 (2013).
Murakami, T. C. et al. A three-dimensional single-cell-resolution whole-brain atlas using CUBIC-X expansion microscopy and tissue clearing. Nat. Neurosci. 21, 625–637 (2018).
Zhang, Y. S. et al. Hybrid microscopy: enabling inexpensive high-performance imaging through combined physical and optical magnifications. Sci. Rep. 6, 22691 (2016).
Aoki, T., Tsuchida, S., Yahara, T. & Hamaue, N. Novel assays for proteases using green fluorescent protein-tagged substrate immobilized on a membrane disk. Anal. Biochem. 378, 132–137 (2008).
Nicholls, S. B. & Hardy, J. A. Structural basis of fluorescence quenching in caspase activatable-GFP. Protein Sci. 22, 247–257 (2013).
Deshpande, T. et al. Subcellular reorganization and altered phosphorylation of the astrocytic gap junction protein connexin43 in human and experimental temporal lobe epilepsy. Glia 65, 1809–1820 (2017).
Crittenden, J. R. et al. Striosome-dendron bouquets highlight a unique striatonigral circuit targeting dopamine-containing neurons. Proc. Natl Acad. Sci. USA 113, 11318–11323 (2016).
Decarreau, J. et al. The tetrameric kinesin Kif25 suppresses pre-mitotic centrosome separation to establish proper spindle orientation. Nat. Cell Biol. 19, 384–390 (2017).
Suofu, Y. et al. Dual role of mitochondria in producing melatonin and driving GPCR signaling to block cytochrome c release. Proc. Natl Acad. Sci. USA 114, E7997–E8006 (2017).
Wang, Y. et al. Combined expansion microscopy with structured illumination microscopy for analyzing protein complexes. Nat. Protoc. 13, 1869–1895 (2018).
Orth, A. et al. Super-multiplexed fluorescence microscopy via photostability contrast. Biomed. Opt. Express 9, 2943–2954 (2018).
Chozinski, T. J. et al. Volumetric, nanoscale optical imaging of mouse and human kidney via expansion microscopy. Sci. Rep. 8, 10396 (2018).
Tsai, A. et al. Nuclear microenvironments modulate transcription from low-affinity enhancers. eLife 6, e28975 (2017).
Jiang, N. et al. Superresolution imaging of Drosophila tissues using expansion microscopy. Mol. Biol. Cell 29, 1413–1421 (2018).
Cahoon, C. K. et al. Superresolution expansion microscopy reveals the three-dimensional organization of the Drosophila synaptonemal complex. Proc. Natl Acad. Sci. USA 114, E6857–E6866 (2017).
Sümbül, U. et al. Automated scalable segmentation of neurons from multispectral images. In Advances in Neural Information Processing Systems 29 (eds Lee, D. D. et al.) 1912–1920 (NIPS Foundation, La Jolla, CA, 2016).
Mosca, T. J., Luginbuhl, D. J., Wang, I. E. & Luo, L. Presynaptic LRP4 promotes synapse number and function of excitatory CNS neurons. eLife 6, 1–29 (2017).
Wang, I. E., Lapan, S. W., Scimone, M. L., Clandinin, T. R. & Reddien, P. W. Hedgehog signaling regulates gene expression in planarian glia. eLife 5, e16996 (2016).
Halpern, A. R., Alas, G. C. M., Chozinski, T. J., Paredez, A. R. & Vaughan, J. C. Hybrid structured illumination expansion microscopy reveals microbial cytoskeleton organization. ACS Nano 11, 12677–12686 (2017).
Artur, C. G. et al. Plasmonic nanoparticle-based expansion microscopy with surface-enhanced Raman and dark-field spectroscopic imaging. Biomed. Opt. Express 9, 603–615 (2018).
Villaseñor, R., Schilling, M., Sundaresan, J., Lutz, Y. & Collin, L. Sorting tubules regulate blood-brain barrier transcytosis. Cell Rep. 21, 3256–3270 (2017).
Li, R., Chen, X., Lin, Z., Wang, Y. & Sun, Y. Expansion enhanced nanoscopy. Nanoscale 10, 17552–17556 (2018).
Treweek, J. B. et al. Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping. Nat. Protoc. 10, 1860–1896 (2015).
Unnersjö-Jess, D. et al. Confocal super-resolution imaging of the glomerular filtration barrier enabled by tissue expansion. Kidney Int. 93, 1008–1013 (2018).
Wei, L. et al. Super-multiplex vibrational imaging. Nature 544, 465–470 (2017).
Hu, F. et al. Supermultiplexed optical imaging and barcoding with engineered polyynes. Nat. Methods 15, 194–200 (2018).
Kumar, A. et al. Influenza virus exploits tunneling nanotubes for cell-to-cell spread. Sci. Rep. 7, 40360 (2017).
Gao, M. et al. Expansion stimulated emission depletion microscopy (ExSTED). ACS Nano 12, 4178–4185 (2018).
Elmore, J. G. et al. Diagnostic concordance among pathologists interpreting breast biopsy specimens. J. Am. Med. Assoc. 313, 1122–1132 (2015).
Choi, H. M. T. et al. Programmable in situ amplification for multiplexed imaging of mRNA expression. Nat. Biotechnol. 28, 1208–1212 (2010).
Choi, H. M. T., Beck, V. A. & Pierce, N. A. Next-generation in situ hybridization chain reaction: higher gain, lower cost, greater durability. ACS Nano 8, 4284–4294 (2014).
Lin, R. et al. A hybridization-chain-reaction-based method for amplifying immunosignals. Nat. Methods 15, 275–278 (2018).
Lee, J. H. et al. Highly multiplexed subcellular RNA sequencing in situ. Science 343, 1360–1363 (2014).
Ke, R. et al. In situ sequencing for RNA analysis in preserved tissue and cells. Nat. Methods 10, 857–860 (2013).
Yoon, Y.-G. et al. Feasibility of 3D reconstruction of neural morphology using expansion microscopy and barcode-guided agglomeration. Front. Comput. Neurosci. 11, 97 (2017).
Lubeck, E. & Cai, L. Single-cell systems biology by super-resolution imaging and combinatorial labeling. Nat. Methods 9, 743–748 (2012).
Lubeck, E., Coskun, A. F., Zhiyentayev, T., Ahmad, M. & Cai, L. Single-cell in situ RNA profiling by sequential hybridization. Nat. Methods 11, 360–361 (2014).
Chen, K. H., Boettiger, A. N., Moffitt, J. R., Wang, S. & Zhuang, X. Spatially resolved, highly multiplexed RNA profiling in single cells. Science 348, aaa6090 (2015).
Moffitt, J. R. et al. High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization. Proc. Natl Acad. Sci. USA 113, 11046–11051 (2016).
Wang, G., Moffitt, J. R. & Zhuang, X. Multiplexed imaging of high-density libraries of RNAs with MERFISH and expansion microscopy. Sci. Rep. 8, 4847 (2018).
Shah, S., Lubeck, E., Zhou, W. & Cai, L. In situ transcription profiling of single cells reveals spatial organization of cells in the mouse hippocampus. Neuron 92, 342–357 (2016).
Wang, Y. et al. Rapid sequential in situ multiplexing with DNA-exchange-imaging in neuronal cells and tissues. Nano Lett. 17, 6131–6139 (2017).
