PittBrains3D: Digital 3D Models for Neuroanatomy Instruction
Overview
This resource presents multiple digital 3D models of the human brain. These models can be downloaded as stl files and either printed or used in digital form.
These models were designed to enrich neuroanatomy instruction. They were designed with undergraduate education in mind, but can be used at multiple levels of instruction.
Digital 3D Models for Neuroanatomy Instruction
These digital 3D models of the human brain, brain cross sections, and internal brain structures were developed to enrich neuroanatomy instruction. They were created by Gage Laporta, under the direction of Dr. Erika Fanselow, in the Department of Neuroscience at the University of Pittsburgh, for use in advanced neuroscience courses.
The models are based on MRI images from the MNI 152 template brain, developed by the Montreal Neurological Institute, and can be downloaded as stl files from GitHub here. These files can be 3D printed or used in digital format.
Models presented in the sections below inlcude:
- Whole brain and hemisected brain
- Brain cross sections in coronal, horizontal, and sagittal planes
- Subcortical forebrain structures (including thalamus, striatum, corpus callosum, hippocampus/hippocampal commissure/amygdala, and the lateral and third ventricles)
- Cerebral vasculature, veins, dural sinuses, and dural reflections
Images of the files are shown in the sections below for reference. Additionally, the last section outlines the process by which these models were developed and resources used. See readme files on GitHub for model dimensions and best practices for printing each type of model.
Acknowledgements: This work was supported by a University of Pittsburgh Provost’s Open Education Resource Award and a dB-SERC Course Transformation Award to EEF. Generous technical support was provided by the University of Pittsburgh Open Lab, Will Hinson, and Sera Thornton.
Whole and hemisected human brain
Digital models available as stl files on GitHub here
Whole brain (including forebrain, cerebellum, brainstem)
Hemisected brain (including forebrain, cerebellum, brainstem)
Brain cross sections in three planes
Digital models available as stl files on GitHub here
Coronal sections
There are 11 coronal sections, numbered starting with the most anterior section, as seen below.
Horizontal sections
There are 9 horizontal sections, numbered starting with the most superior section, as seen below.
Sagittal sections
There are 10 sagittal sections, five in the left hemisphere (1L-5L), and five in the right (1R-5R). For both hemispheres, numbering begins laterally and goes medially.
Note that the locations of the cuts we used for these cross sections were chosen carefully to display specific structures that are often relevant for teaching neuroanatomy. As a result, the cross sections are of varying thicknesses. Additionally, the left and right hemisphere sagittal plane cross sections are not identical; they were deliberately chosen to display different parasagittal views of the brain on each side.
Subcortical forebrain structures
Digital models available as stl files on GitHub here
- Thalami
- Striatum
- Corpus callosum
- Hippocampus + hippocampal commissure + amygdala
- Lateral and third ventricles
Cerebral vasculature, dural reflections, and dural sinuses
Digital models available as stl files on GitHub here
- Cerebral arteries
- Cerebral veins + superior and inferior sagittal sinuses
- Dural sinuses + reflections
- All structures + brain hemisphere
Structures shown together:
Structures shown individually:
Brainstem and axial brainstem cross sections
Models available as stl files on GitHub here
Brainstem alone
Brainstem + vasculature
Brainstem + cranial nerves
Brainstem axial cross sections
Information about how these models were developed
These models are based on a standard brain template known as the MNI152 (a.k.a. ICBM152) template, which was developed at the Montreal Neurological Institute. This template is based on an average of MRI images from 152 normal adult human brains (i.e. no known brain-related disease). This template and variations on it are commonly used by researchers and clinicians in a range of applications (Mandal et al., 2012). Advantages of basing our models on the MNI152 template include that the models are a consistent size and shape; the models are not derived from a single brain that may not be representative; and 2D images of the MNI152 brain are available in MRI format.
Link to MNI-IBCM templates (several variations):
https://nist.mni.mcgill.ca/atlases/
Copyright (C) 1993–2009 Louis Collins, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University
These cross sections are based on T1-weighted MRI images from the MNI-152 template brain. In order to construct the 3D cross section models, Gage Laporta, a former neuroscience student at the University of Pittsburgh, converted the grayscale MRI images into heightmaps which could subsequently be converted into a 3D mesh. Gage then optimized the mesh structures using 3D modeling software to develop the current files, under the direction of Dr. Erika Fanselow. We emphasized structures in the models that are frequently covered in undergraduate neuroanatomy courses, though these models could be used at many levels of instruction.
Reference:
Mandal PK, Mahakjan R, & Dinov ID (2012) Structural brain atlases: design, rationale, and applications in normal and pathological cohorts. Journal of Alzheimer’s Disorders, 31 (0 3)