Apr 08, 2026

Brain dissection protocol

DOI
https://dx.doi.org/10.17504/protocols.io.261gedq8ov47/v1
  • 1KU Leuven
Hanne HD Dhondt
Icon indicating open access to content
QR code linking to this content
DOI: https://dx.doi.org/10.17504/protocols.io.261gedq8ov47/v1
Protocol Citation: Ana Cascalho, Nina Schoonvliet 2026. Brain dissection protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.261gedq8ov47/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: January 13, 2024
Last Modified: April 09, 2026
Protocol  Integer ID: 96554
Keywords: brain dissection protocol this protocol, brain dissection protocol, brain dissection, protocol, protocol detail
Abstract
This protocol details the brain dissection.
Attachments
Icon for Brain dissection protocol.docx
Brain dissection pro...
16KB
Materials
  • Liquid Nitrogen (for snap freezing)
  • Ice box with plastic protection
  • Collection tubes (1,5ml) with appropriate labels (Note: to withstand the liquid nitrogen the label should go over each other to seal the glue). Tubes should also be number labelled to avoid sample loss if a label detaches)
  • Gelatin Plate for dissection with pins + Ice cold DPBS (Sigma; D8662).
  • Dissection kit:
1. Scissors:
  • Large (Cervical dislocation/Decapitation)
  • Curved/Medium/Thin (Tissue isolation)
  • Bone (Adult bone/skull separation)
2. Forceps:
  • Large/Medium (organ manipulation)
  • Thin (N3/N5) (tissue dissection and subdissection)
3. Scalpels (manual and with holder)
4. Bags for tissue leftovers.
  • Needle Container
  • Cleaning sponge and detergent for washing materials post dissection.
Preparation
Ensure all tools and materials are sterilized.
Set up a clean and organized workspace.
Wear appropriate personal protective equipment like a lab coat and gloves.
Mouse Sacrifice
Use cervical dislocation (no use of anesthesia to minimize anesthesia-related effects).
With surgical scissors, remove the head by cutting posterior from the ears.
Skin Incision
Make a midline incision in the skin using scissors.
Flip the skin over the eyes to expose the skull.
Skull Incision
Use Iris scissors to make a small incision on the top of the skull, starting from the caudal part at the point of the (inter)parietal bone.
Be cautious not to cut through the brain tissue.
Frontal Bone Cut
Make a firm cut through the most anterior part of the skull, between the eyes (frontal bone).
Note
This facilitates easier brain removal.

Parietal Bone Removal
Tilt one side of the parietal bone with the curved narrow pattern forceps and break it off.
Repeat for the other side.
If the frontal bone remains, make a small incision to facilitate its removal.
Be careful not to damage the meninges between the brain and the skull.
Brain Extraction
Once the brain is free from meninges, slide the closed curved narrow pattern forceps under the anterior part of the brain (olfactory bulb).
Gently tilt the forceps upward to lift the brain.
Slide the forceps further down to break optic nerves and other cranial nerves.
Lift the brain out of the skull gently.
Brain Washing
Wash the brain thoroughly with ice-cold DPBS (Sigma; D8662) on the gelatin plate.
Brain Dissection
Cut the brain into left and right hemisphere (OR DO THE NEXT STEP).
Depending on the regions of interest, dissect the following areas:

  • Cerebellum
  • Cortex
  • Interbrain
  • Hindbrain
Freezing
Place dissected brain parts in labeled tubes.
Snap freeze the tubes in liquid nitrogen.
Note
  • Always handle the tissues carefully to avoid damage.
  • Work quickly to preserve tissue integrity.
  • Store frozen brain parts at -80 °C until further analysis.