Feb 05, 2026

Public workspaceHuman Brain Tissue Processing 

DOI
https://dx.doi.org/10.17504/protocols.io.8epv55dxdv1b/v1
  • Anastasia Filimontseva1,2,
  • YuHong Fu1,2,
  • Glenda Halliday1,2
  • 1Brain and Mind Centre & Faculty of Medicine and Health School of Medical Sciences, The University of Sydney, Sydney, NSW 2050, Australia;
  • 2Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
Anastasia Filimontseva
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DOI: https://dx.doi.org/10.17504/protocols.io.8epv55dxdv1b/v1
Protocol Citation: Anastasia Filimontseva, YuHong Fu, Glenda Halliday 2026. Human Brain Tissue Processing . protocols.io https://dx.doi.org/10.17504/protocols.io.8epv55dxdv1b/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: February 04, 2026
Last Modified: February 06, 2026
Protocol Integer ID: 242653
Keywords: ASAPCRN, standard processing for ffpe human midbrain tissue section, ffpe human midbrain tissue section, human brain tissue processing, ffpe, standard processing
Funders Acknowledgements:
Aligning Science Across Parkinson's
Grant ID: ASAP-020505
National Health and Medical Research Council Investigator Grant
Grant ID: 1176607
Abstract
Standard processing for FFPE human midbrain tissue sections.
Troubleshooting
6µm formalin-fixed paraffin-embedded (FFPE) section preparation
FFPE cross-sectional midbrain tissue blocks from healthy controls without neurological or neuropathological diseases were obtained from the Sydney Brain Bank (n=10).
These tissue blocks were sectioned on a microtime at 6µm.
Sections were dried on microscope slides at 37°C for 48 hours.
Routine deparaffinization and dehydration procedure followed prior to immunohistochemical staining (10.17504/protocols.io.e6nvwnm57vmk/v1).
50µm serial section preparation
Formalin-fixed healthy control brainstems (n=4) were blocked transversely and postfixed for 24 hours at 4°C.
Blocks were cryoprotected in 30% buffered sucrose.

Blocks were sectioned on a freezing microtome at 50µm.
Nissl staining on 50µm serial sections
Sections at 750µm intervals were stained with 0.5% cresyl violet (HB5608 Hello Bio).