Frequently Asked Questions About Imaging Cleared Tissues

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Courtney Akitake Ph.D Product Marketing Manager - Lightsheet
ZEISS Microscopy

This presentation addresses five frequently asked questions that typically arise while preparing and imaging optically cleared tissue samples with Lightsheet and other microscopes:

  1. Why do I need to clear my sample?
  2. What clearing method should I use?
  3. How do I image my sample after clearing?
  4. How can I improve my image quality?
  5. How do I manage all the data?

The information presented here is intended to serve as an introductory overview for researchers that are just getting into tissue clearing, as well as a reference for more advanced individuals that want to optimize imaging of their already cleared samples.


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Light sheet fluorescence microscopy (LSFM) with its unique illumination principle allows fast and gentle imaging of whole living model organisms, tissues, and developing cells. The high stability of ZEISS Lightsheet 7 enables researchers to observe living samples over extended periods of time – even days – with less phototoxicity than ever before. The new light sheet microscope can also be used to image very large optically cleared specimens in toto, and with subcellular resolution. The dedicated optics, sample chambers, and sample holders of ZEISS Lightsheet 7 can be adjusted to the refractive index of the chosen clearing method to observe large samples, even whole mouse brains.