Neuroscience JoVE (Open Access) Citable · DOI

Utilizing 3D Printing Technology to Merge MRI with Histology: A Protocol for Brain Sectioning

Name: Utilizing 3D Printing Technology to Merge MRI with Histology: A Protocol for Brain Sectioning
Uploaded: 2026-06-17
Duration: 15 min 53 s
Description: Magnetic resonance imaging (MRI) allows for the delineation between normal and abnormal tissue on a macroscopic scale, sampling an entire tissue volume ...

DOI: 10.3791/54780-v

What you'll learn

✓ Design and 3D-print custom brain holders for precise MRI-to-histology alignment
✓ Extract brain surface contours from MRI volumes using imaging software
✓ Create accurate blade maps to guide reproducible brain sectioning

Protocol

The overall goal of this protocol is to accurately align magnetic resonance imaging (MRI) image volumes with histology sections via the creation of customized 3D-printed brain holders and slicer boxes.

Difficulty

advanced

Total time

~3–4 days per brain (MRI acquisition ~1 day, 3D printing ~1–2 days, sectioning ~2–4 hours)

Model organism

Mouse

Steps

Acquire and prepare MRI brain image volumes

Perform MRI scanning of the intact brain and acquire high-resolution image stacks for volumetric analysis and surface extraction.

▶ 00:36

Extract brain surface from MRI volume

Segment and isolate the brain surface contours from the 3D MRI dataset to define the anatomical boundaries.

▶ 01:53

Select and define slice plane locations

Choose anatomically relevant coronal, sagittal, or axial planes and define precise slice coordinates within the MRI volume.

▶ 04:06

Create MRI-based blade positioning map

Generate a 2D map encoding blade spacing and angles relative to MRI coordinates to ensure accurate sectioning alignment.

▶ 05:05

Image brain and blade gap surfaces

Acquire high-resolution photographs of the brain surface and blade gap geometry to calibrate spatial relationships for 3D printing.

▶ 05:46

Edit and refine brain contour boundaries

Manually adjust segmented brain contours in imaging software to correct any segmentation errors and ensure anatomical accuracy.

▶ 07:27

Design 3D-printable brain slicer box

Convert MRI-derived contours and blade maps into a CAD model suitable for 3D printing that will hold and guide the brain during sectioning.

▶ 07:50

Print custom brain slicer box

3D-print the designed slicer box using appropriate resin or plastic materials and allow adequate curing time.

▶ 11:25

Section brain using printed slicer box

Position the brain in the 3D-printed holder and cut serial sections along the pre-defined blade planes using a vibratome or cryostat.

▶ 12:16

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