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Salamanders pp 123–133Cite as

Ethyl Cinnamate-Based Tissue Clearing Strategies

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Part of the Methods in Molecular Biology book series (MIMB,volume 2562)


Tissue clearing turns otherwise turbid and opaque tissue transparent, enabling imaging deep within tissues. The nontransparent nature of most tissues is due to the refractive index mismatch between its three major constituent components (lipids, proteins, and water). All tissue clearing methods rectify this mismatch by homogenizing the refractive index within the tissue and carefully matching it to the surrounding media. Here we describe a detailed protocol to clear a wide range of salamander tissues. We also include several optional steps such as depigmentation, antibody staining, and tissue mounting. These steps are optional, and do not change anything in the steps needed for tissue clearing. Depending on the fluorescent signal and optics employed, images up to several millimeters inside of the tissue can be acquired.

Key words

  • Tissue clearing
  • Dehydration
  • Ethyl cinnamate
  • Antibody staining

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This work was supported by an Austrian Science Fund Lise Meitner Fellowship (M2444) to W.M. and a European Research Council Advanced Grant (742046) and a Deutsche Forschungsgemeinschaft grant (TA 274/13-1) to E.M.T.

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Correspondence to Wouter Masselink .

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Masselink, W., Tanaka, E.M. (2023). Ethyl Cinnamate-Based Tissue Clearing Strategies. In: Seifert, A.W., Currie, J.D. (eds) Salamanders. Methods in Molecular Biology, vol 2562. Humana, New York, NY.

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2658-0

  • Online ISBN: 978-1-0716-2659-7

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