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Related Experiment Video

Updated: Dec 18, 2025

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A versatile depigmentation, clearing, and labeling method for exploring nervous system diversity.

Marko Pende1,2, Karim Vadiwala3, Hannah Schmidbaur4

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|June 12, 2020
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Summary
This summary is machine-generated.

A new DEpigmEntation-Plus-Clearing (DEEP-Clear) method removes natural pigmentation, enabling deep imaging of previously inaccessible biological specimens. This technique allows for detailed visualization of organs and subcellular structures across diverse species.

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Area of Science:

  • Biological imaging
  • Histology
  • Biotechnology

Background:

  • Classical histology and current tissue clearing methods struggle with pigmented biological specimens.
  • Natural pigmentation hinders deep imaging of organs and whole organisms.

Purpose of the Study:

  • To develop a rapid tissue clearing method that overcomes natural pigmentation challenges.
  • To enable advanced imaging techniques for a wider range of biological samples.

Main Methods:

  • Developed a fast DEpigmEntation-Plus-Clearing (DEEP-Clear) method.
  • Integrated DEEP-Clear into existing workflows.
  • Combined whole-system labeling with techniques like immunohistochemistry, RNA in situ hybridization, EdU labeling, and transgenic marker visualization.
  • Utilized light-sheet and confocal microscopy for imaging.

Main Results:

  • Successfully cleared and imaged pigmented organs and whole animals.
  • Achieved unprecedented insight into eyes, nervous systems, and subcellular structures.
  • Demonstrated applicability across diverse model organisms including worms, squids, axolotls, and zebrafish.
  • DEEP-Clear is compatible with various detection methods.

Conclusions:

  • DEEP-Clear is an effective and versatile method for imaging pigmented biological specimens.
  • This technique expands the scope of deep imaging to new species and developmental stages.
  • Facilitates exploration of biological diversity previously limited by imaging constraints.