Mar 20, 2026
Brain Microdissection in Mouse Models
- 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. Brain Microdissection in Mouse Models. protocols.io https://dx.doi.org/10.17504/protocols.io.36wgqxq1ylk5/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: 313190
Keywords: brain microdissection, mouse brain, mouse models, brain regions, brain microdissection in mouse model, mouse brain hemisphere, method for the microdissection, microdissection, subsequent analysis of specific brain region, specific brain region, mouse model
Funders Acknowledgements:
NIH General Medical Sciences
Grant ID: P20GM152335
Abstract
This protocol describes a method for the microdissection of a mouse brain hemisphere that allows for subsequent analysis of specific brain regions.
Materials
Microdissection microscope
Weigh boat
Scalpel
Forceps
Fine tip thumb forceps
Troubleshooting
Problem
Contaminated specimens
Solution
Review anatomy and use sharp tools to ensure quality extractions. Pay special attention to natural tissue separation.
Problem
Extreme manipulations of specimens
Solution
Start with minimal contact of tissues to feel for tissues changes.
Problem
Failure to isolate regions
Solution
Utilize a dissection microscope or other instrument that would improve field of view.
Mouse Brain Microdissection
Note
The following procedure was performed under a microdissection microscope. Full dissection shown in Fig 1. See Fig 2 for a size reference of the mouse brain hemisphere after separation.
Figure 1. Completed Microdissection of the Mouse Brain. Labeled brain regions following careful dissection including the olfactory bulb, thalamus, hippocampus, striatum, brainstem, cerebellum, and cortex. Created in BioRender. Seerley, A. (2025) https://BioRender.com/v5y4pwe
Figure 2. Size Reference of the Mouse Brain. Lateral-medial view of a fixed right hemisphere mouse brain. [A] Measuring approximately ~1.9cm in length and [B]~0.6cm in height.
Hemispheric Separation - Place the brain on a clean surface with the dorsal side facing up (ventral side facing down) (Fig 3A). Using the scalpel, make a sagittal cut along the longitudinal fissure to separate the hemispheres.
Figure 3. Brain Microdissection. Panel [A] shows the right hemisphere. [B] Thalamus, [C&D] Hippocampus, [E&F] Striatum, [G]Cortex, [H] Cerebellum, [I] Brainstem, [J] Olfactory bulb. (Zeiss Stemi 508 & Axiocam 208 Color Photo).
Thalamus - On the medial side of the brain while holding the hemisphere steady with forceps, visualize and scoop out the thalamus with the scalpel using blunt dissection, paying attention to region boundaries, see Fig 3B.
Hippocampus - On the medial side of the brian, peel the cortex laterally, perpendicular to the midline using blunt dissection with the scalpel and while holding the hippocampus in place with the forceps to ensure separation of the two regions. Perform blunt dissection to extract the hippocampus medially toward the midline using the scalpel, see Fig 3C and D.
Striatum - Expose the striatum by removing the cortex and hippocampus as described above. Incise around the perimetere of the striatum with fine tip thumb forceps. Using the scalpel, scoop out the striatum with reference to natural tissue separtation, see Fig 1E and F. Striations help to differentiate the striatum from the cortex.
Cortex - Excise the base of the already dissected cortex using the scalpel blade, see Fig 10G.
Cerebellum - Remove the base of the cerebellum from the rest of the brain using a scalpel with attention to natural separation, see Fig 10H.
Brainstem - Excise the brainstem from the midbrain, see Fig 10I.
Olfactory bulb - Excise the olfactory bulb from the forebrain, see Fig 10J.