Asteriti, S., Ricci, V., & Cangiano, L. (2020). Two simple criteria to estimate an objective’s performance when imaging in non design tissue clearing solutions. Journal of Neuroscience Methods, 332, 108564–108564. https://doi.org/10.1016/j.jneumeth.2019.108564
Azaripour, A., Lagerweij, T., Scharfbillig, C., Jadczak, A. E., Willershausen, B., & Van Noorden, C. J. F. (2016). A survey of clearing techniques for 3D imaging of tissues with special reference to connective tissue. Progress in Histochemistry and Cytochemistry, 51(2), 9–23. https://doi.org/10.1016/j.proghi.2016.04.001
Becher, T., Riascos-Bernal, D. F., Kramer, D. J., Almonte, V. M., Chi, J., Tong, T., Oliveira-Paula, G. H., Koleilat, I., Chen, W., Cohen, P., & Sibinga, N. E. . (2020). Three-Dimensional Imaging Provides Detailed Atherosclerotic Plaque Morphology and Reveals Angiogenesis After Carotid Artery Ligation. Circulation Research, 126(5), 619–632. https://doi.org/10.1161/CIRCRESAHA.119.315804
Bèchet, N. B., Kylkilahti, T. M., Mattsson, B., Petrasova, M., Shanbhag, N. C., & Lundgaard, I. (2020). Light sheet fluorescence microscopy of optically cleared brains for studying the glymphatic system. Journal of Cerebral Blood Flow and Metabolism, 40(10), 1975–1986. https://doi.org/10.1177/0271678X20924954
Brenna, C., Khan, A. ul M., Picascia, T., Sun, Q., Heuveline, V., & Gretz, N. (2020). New technical approaches for 3D morphological imaging and quantification of measurements. Anatomical Record (Hoboken, N.J. : 2007), 303(10), 2702–2715. https://doi.org/10.1002/ar.24463
Chi, J., Wu, Z., Choi, C. H. J., Nguyen, L., Tegegne, S., Ackerman, S. E., Crane, A., Marchildon, F., Tessier-Lavigne, M., & Cohen, P. (2018). Three-Dimensional Adipose Tissue Imaging Reveals Regional Variation in Beige Fat Biogenesis and PRDM16-Dependent Sympathetic Neurite Density. Cell Metabolism, 27(1), 226–236.e3. https://doi.org/10.1016/j.cmet.2017.12.011
Costantini, I., Cicchi, R., Silvestri, L., Vanzi, F., & Pavone, F. S. (2019). In-vivo and ex-vivo optical clearing methods for biological tissues: review. Biomedical Optics Express, 10(10), 5251–5267. https://doi.org/10.1364
Du, H., Hou, P., Zhang, W., & Li, Q. (2018). Advances in CLARITY-based tissue clearing and imaging. Experimental and Therapeutic Medicine, 16(3), 1567–1576. https://doi.org/10.3892/etm.2018.6374
Du, H., Hou, P., Zhang, W., & Li, Q. (2018). Advances in CLARITY-based tissue clearing and imaging. Experimental and Therapeutic Medicine, 16(3), 1567–1576. https://doi.org/10.3892/etm.2018.6374
Goranci-Buzhala, G., Mariappan, A., Gabriel, E., Ramani, A., Ricci-Vitiani, L., Buccarelli, M., D’Alessandris, Q. G., Pallini, R., & Gopalakrishnan, J. (2020). Rapid and Efficient Invasion Assay of Glioblastoma in Human Brain Organoids. Cell Reports (Cambridge), 31(10), 107738–107738. https://doi.org/10.1016/j.celrep.2020.107738
Henning, Y., Osadnik, C., & Malkemper, E. P. (2019). EyeCi: Optical clearing and imaging of immunolabeled mouse eyes using light-sheet fluorescence microscopy. Experimental Eye Research, 180, 137–145. https://doi.org/10.1016/j.exer.2018.12.001
Jährling, N., Becker, K., Saghafi, S., & Dodt, H.-U. (n.d.). Light-Sheet Fluorescence Microscopy: Chemical Clearing and Labeling Protocols for Ultramicroscopy. Light Microscopy, 33–49. https://doi.org/10.1007
Jing, D., Yi, Y., Luo, W., Zhang, S., Yuan, Q., Wang, J., Lachika, E., Zhao, Z., & Zhao, H. (2019). Tissue Clearing and Its Application to Bone and Dental Tissues. Journal of Dental Research, 98(6), 621–631. https://doi.org/10.1177/0022034519844510/978-1-4939-6810-7_3
Jing, D., Zhang, S., Luo, W., Gao, X., Men, Y., Ma, C., Liu, X., Yi, Y., Bugde, A., Zhou, B. O., Zhao, Z., Yuan, Q., Feng, J. Q., Gao, L., Ge, W.-P., & Zhao, H. (2018). Tissue clearing of both hard and soft tissue organs with the PEGASOS method. Cell Research, 28(8), 803–818. https://doi.org/10.1038/s41422-018-0049-z
Kakimoto, T. (2018). Validation of an easily applicable three-dimensional immunohistochemical imaging method for a mouse brain using conventional confocal microscopy. Histochemistry and Cell Biology, 149(1), 97–103. https://doi.org/10.1007/s00418-017-1614-0
Kaufman, J. A., Castro, M. J., Ruiz, S. A., Jentarra, G. M., Chavira, B., & Rodriguez-Sosa, J. R. (2020). Clearing, immunofluorescence, and confocal microscopy for the three-dimensional imaging of murine testes and study of testis biology. Journal of Structural Biology, 209(3), 107449–107449. https://doi.org/10.1016/j.jsb.2020.107449
Kurihara, D., Mizuta, Y., Sato, Y., & Higashiyama, T. (2015). ClearSee: a rapid optical clearing reagent for whole-plant fluorescence imaging. Development (Cambridge), 142(23), 4168–4179. https://doi.org/10.1242/dev.127613
Lagoutte, E., Villeneuve, C., Fraisier, V., Krndija, D., Deugnier, M.-A., Chavrier, P., & Rosse, C. (2020). A new pipeline for pathophysiological analysis of the mammary gland based on organoid transplantation and organ clearing. Journal of Cell Science, 133(12), jcs242495. https://doi.org/10.1242/jcs.242495
Li, Y., Xu, J., Wan, P., Yu, T., & Zhu, D. (2018). Optimization of GFP Fluorescence Preservation by a Modified uDISCO Clearing Protocol. Frontiers in Neuroanatomy, 12, 67–67. https://doi.org/10.3389/fnana.2018.00067
Matryba, P., Bozycki, L., Pawłowska, M., Kaczmarek, L., & Stefaniuk, M. (2018). Optimized perfusion‐based CUBIC protocol for the efficient whole‐body clearing and imaging of rat organs. Journal of Biophotonics, 11(5), e201700248–n/a. https://doi.org/10.1002/jbio.201700248
Matsumoto, K., Mitani, T. T., Horiguchi, S. A., Kaneshiro, J., Murakami, T. C., Mano, T., Fujishima, H., Konno, A., Watanabe, T. M., Hirai, H., & Ueda, H. R. (2019). Advanced CUBIC tissue clearing for whole-organ cell profiling. Nature Protocols, 14(12), 3506–3537. https://doi.org/10.1038/s41596-019-0240-9
McKey, J., Cameron, L. A., Lewis, D., Batchvarov, I. S., & Capel, B. (2020). Combined iDISCO and CUBIC tissue clearing and lightsheet microscopy for in toto analysis of the adult mouse ovary. Biology of Reproduction, 102(5), 1080–1089. https://doi.org/10.1093/biolre/ioaa012
Mizuta, Y., & Tsuda, K. (n.d.). Three-Dimensional Multiphoton Imaging of Transcription Factor by ClearSee. Plant Transcription Factors, 257–268. https://doi.org/10.1007/978-1-4939-8657-6_15
Muntifering, M., Castranova, D., Gibson, G. A., Meyer, E., Kofron, M., & Watson, A. M. (2018). Clearing for Deep Tissue Imaging. Current Protocols in Cytometry, 86(1), e38–n/a. https://doi.org/10.1002/cpcy.38
Musielak, T. J., Slane, D., Liebig, C., & Bayer, M. (2016). A Versatile Optical Clearing Protocol for Deep Tissue Imaging of Fluorescent Proteins in Arabidopsis thaliana. PloS One, 11(8), e0161107–e0161107. https://doi.org/10.1371/journal.pone.0161107
Pende, M., Vadiwala, K., Schmidbaur, H., Stockinger, A. W., Murawala, P., Saghafi, S., Dekens, M. P. S., Becker, K., Revilla-I-Domingo, R., Papadopoulos, S.-C., Zurl, M., Pasierbek, P., Simakov, O., Tanaka, E. M., Raible, F., & Dodt, H.-U. (2020). A versatile depigmentation, clearing, and labeling method for exploring nervous system diversity. Science Advances, 6(22), eaba0365–eaba0365. https://doi.org/10.1126/sciadv.aba0365
Puelles, V. G., Moeller, M. J., & Bertram, J. F. (2017). We can see clearly now: optical clearing and kidney morphometrics. Current Opinion in Nephrology and Hypertension, 26(3), 179–186. https://doi.org/10.1097/MNH.0000000000000314
Susaki, E. A., Shimizu, C., Kuno, A., Tainaka, K., Li, X., Nishi, K., Morishima, K., Ono, H., Ode, K. L., Saeki, Y., Miyamichi, K., Isa, K., Yokoyama, C., Kitaura, H., Ikemura, M., Ushiku, T., Shimizu, Y., Saito, T., Saido, T. C., … Ueda, H. R. (2020). Versatile whole-organ/body staining and imaging based on electrolyte-gel properties of biological tissues. Nature Communications, 11(1), 1982–1982. https://doi.org/10.1038/s41467-020-15906-5
Ueda, H. R., Dodt, H.-U., Osten, P., Economo, M. N., Chandrashekar, J., & Keller, P. J. (2020). Whole-Brain Profiling of Cells and Circuits in Mammals by Tissue Clearing and Light-Sheet Microscopy. Neuron (Cambridge, Mass.), 106(3), 369–387. https://doi.org/10.1016/j.neuron.2020.03.004
Ueda, H. R., Ertuerk, A., Chung, K., Gradinaru, V., Chedotal, A., Tomancak, P., & Keller, P. J. (2020). Tissue clearing and its applications in neuroscience. Nature Reviews. Neuroscience, 21(2), 61–79. https://doi.org/10.1038/s41583-019-0250-1
Ursache, R., Andersen, T. G., Marhavý, P., & Geldner, N. (2018). A protocol for combining fluorescent proteins with histological stains for diverse cell wall components. The Plant Journal : for Cell and Molecular Biology, 93(2), 399–412. https://doi.org/10.1111/tpj.13784
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Xu, N., Tamadon, A., Liu, Y., Ma, T., Leak, R. K., Chen, J., Gao, Y., & Feng, Y. (2017). Fast free-of-acrylamide clearing tissue (FACT)-an optimized new protocol for rapid, high-resolution imaging of three-dimensional brain tissue. Scientific Reports, 7(1), 9895–15. https://doi.org/10.1038/s41598-017-10204-5
Zhang, H., Yarinome, K., Kawakami, R., Otomo, K., Nemoto, T., & Okamura, Y. (2020). Nanosheet wrapping-assisted coverslip-free imaging for looking deeper into a tissue at high resolution. PloS One, 15(1), e0227650–e0227650. https://doi.org/10.1371/journal.pone.0227650
Imaging RNA
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Buxbaum, A. R., Yoon, Y. J., Singer, R. H., & Park, H. Y. (2015). Single-molecule insights into mRNA dynamics in neurons. Trends in Cell Biology, 25(8), 468–475. https://doi.org/10.1016/j.tcb.2015.05.005
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Stereology
Kubínová, L., & Janáček, J. (2001). Confocal microscopy and stereology: Estimating volume, number, surface area and length by virtual test probes applied to three-dimensional images. Microscopy Research and Technique, 53(6), 425–435. https://doi.org/10.1002/jemt.1112
