Mar 20, 2026
Mouse Brain Extraction
- Lilia Crew1,
- Alyssa Seerley2,
- Serena McElroy2,
- Andrea Grindeland Panter1,2
- 1Touro University College of Osteopathic Medicine, Great Falls, MT, United States;
- 2Weissman Hood Institute at Touro University, McLaughlin Research Institute, Great Falls, MT, United States
- Lilia Crew: Co-first author;
- Alyssa Seerley: Co-first author
- Andrea Grindeland Panter: Senior author
Protocol Citation: Lilia Crew, Alyssa Seerley, Serena McElroy, Andrea Grindeland Panter 2026. Mouse Brain Extraction. protocols.io https://dx.doi.org/10.17504/protocols.io.6qpvrbqy3lmk/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 12, 2026
Last Modified: March 20, 2026
Protocol Integer ID: 313182
Keywords: Mouse, brain extraction, mouse brain extraction this protocol, mouse brain extraction, intact mouse brain, method for the extraction, extraction, downstream analysis
Funders Acknowledgements:
NIH General Medical Sciences
Grant ID: P20GM152335
Abstract
This protocol describes a method for the extraction of an intact mouse brain to be used for downstream analysis.
Materials
70% EtOH
Large scissors
Small scissors
Forceps
Troubleshooting
Problem
Poor skull exposure
Solution
Confirm full exposure by viewing all sides of the mouse brain before trying to remove it from the body.
Problem
Brain damaged
Solution
Confirm proper instrument and take extra precautions to avoid unnecessary handling of the brain.
Problem
Dissection at warm room temperature leading to poor quality specimens
Solution
Use ice or a cool surface underneath the brain. Transfer specimen to ice when no longer in use. Be careful not to freeze tissue during dissection.
Mouse Brain Extraction
Place the mouse in a ventral position
Spray the cranium with 70% EtOH to wet the hair down
Using a sharp pair of large scissors cut transversely immediately caudal to the occiput. Discard the body appropriately. If removal of the head from the body is desired, follow this step. If not, go to step 4.
Incise the cutaneous layers using the small scissors in a midline sagittal cut extending from caudal occiput to the rostrum, see Fig 1A. Displace the skin tissue laterally to visualize the skull.
Figure 1. Brain Extraction. [A] Midline sagittal skin incision from occiput to rostrum. [B] Transverse incision between the orbitals. [C] Skull cut from occiput to orbit in a rostral direction. [D] Lateral separation of skull from brain. Created in BioRender. Seerley, A. (2025) https://BioRender.com/k5txf1t
Place the tips of the small scissors in the orbitals and cut the skull transversely as seen in Fig 1B.
Fixing the tips of the small scissors under the occiput of the skull, with slow rostral progression, cut on the midline with small precise movements to the previous orbit incision, see Fig. 1C.
Placing the forceps under the skull at the incision on the left side, grip and pull the skull laterally, perpendicular to the midline, peeling the skull from the brain, see Fig. 1D.
If the skull breaks into pieces, remove each piece individually until complete hemisphere exposure is acheived.
Repeat steps 7 and 8 on the right hemisphere.
Once full brain exposure is accomplished, place the forceps beneath the brainstem and excise the brain by gently pulling superiorly and rostrally. Inverting the mouse so that the dorsal surface of the cranium is closest to the workbench can be helpful, as it allows gravity to assist in brain extraction.