Mar 31, 2026

Light Sheet Fluorescent Microscopy Sectioning from FFPE

DOI
https://dx.doi.org/10.17504/protocols.io.ewov1rk22lr2/v1
  • 1Stanford University
  • Human BioMolecular Atlas Program (HuBMAP) Method Development Community
    Tech. support email: [email protected]
Joanna Bi
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DOI: https://dx.doi.org/10.17504/protocols.io.ewov1rk22lr2/v1
Protocol Citation: Joanna Bi 2026. Light Sheet Fluorescent Microscopy Sectioning from FFPE. protocols.io https://dx.doi.org/10.17504/protocols.io.ewov1rk22lr2/v1
License: This is an open access  protocol  distributed under the terms of the  Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: March 30, 2026
Last Modified: April 15, 2026
Protocol  Integer ID: 314145
Keywords: blocks for light sheet fluorescent microscopy, light sheet fluorescent microscopy, ffpe protocol for processing, ffpe protocol, sectioning formalin, fixed paraffin, embedded block
Abstract
Protocol for processing and sectioning formalin-fixed paraffin-embedded blocks for light sheet fluorescent microscopy.
Bake FFPE block at 60°C for 2 hours
Dewax tissue in xylene
Rehydrate tissue from ethanol to PBS
Embed tissue in 8% agarose
Section tissue with a vibratome at 1mm