Localization of Metal Electrodes in the Intact Rat Brain Using Registration of 3D Microcomputed Tomography Images to a Magnetic Resonance Histology Atlas.
Abstract
Simultaneous neural recordings taken from multiple areas of the rodent brain are garnering
growing interest due to the insight they can provide about spatially distributed neural
circuitry. The promise of such recordings has inspired great progress in methods for
surgically implanting large numbers of metal electrodes into intact rodent brains.
However, methods for localizing the precise location of these electrodes have remained
severely lacking. Traditional histological techniques that require slicing and staining
of physical brain tissue are cumbersome, and become increasingly impractical as the
number of implanted electrodes increases. Here we solve these problems by describing
a method that registers 3-D computerized tomography (CT) images of intact rat brains
implanted with metal electrode bundles to a Magnetic Resonance Imaging Histology (MRH)
Atlas. Our method allows accurate visualization of each electrode bundle's trajectory
and location without removing the electrodes from the brain or surgically implanting
external markers. In addition, unlike physical brain slices, once the 3D images of
the electrode bundles and the MRH atlas are registered, it is possible to verify electrode
placements from many angles by "re-slicing" the images along different planes of view.
Further, our method can be fully automated and easily scaled to applications with
large numbers of specimens. Our digital imaging approach to efficiently localizing
metal electrodes offers a substantial addition to currently available methods, which,
in turn, may help accelerate the rate at which insights are gleaned from rodent network
neuroscience.
Type
Journal articlePermalink
https://hdl.handle.net/10161/10327Published Version (Please cite this version)
10.1523/ENEURO.0017-15.2015Publication Info
Borg, Jana Schaich; Vu, Mai-Anh; Badea, Cristian; Badea, Alexandra; Johnson, G Allan;
& Dzirasa, Kafui (2015). Localization of Metal Electrodes in the Intact Rat Brain Using Registration of 3D
Microcomputed Tomography Images to a Magnetic Resonance Histology Atlas. eNeuro, 2(4). 10.1523/ENEURO.0017-15.2015. Retrieved from https://hdl.handle.net/10161/10327.This is constructed from limited available data and may be imprecise. To cite this
article, please review & use the official citation provided by the journal.
Collections
More Info
Show full item recordScholars@Duke
Alexandra Badea
Associate Professor in Radiology
I have a joint appointment in Radiology and Neurology and my research focuses on neurological
conditions like Alzheimer’s disease. I work on imaging and analysis to provide a comprehensive
characterization of the brain. MRI is particularly suitable for brain imaging, and
diffusion tensor imaging is an important tool for studying brain microstructure, and
the connectivity amongst gray matter regions. I am interested in image segmentation,
morphometry and shape ana
Cristian Tudorel Badea
Professor in Radiology
Our lab's research focus lies primarily in developing novel quantitative imaging systems,
reconstruction algorithms and analysis methods. My major expertise is in preclinical
CT.
Currently, we are particularly interested in developing novel strategies for spectral
CT imaging using nanoparticle-based contrast agents for theranostics (i.e. therapy
and diagnostics).
We are also engaged in developin
Kafui Dzirasa
K. Ranga Rama Krishnan Associate Professor
G. Allan Johnson
Charles E. Putman University Distinguished Professor of Radiology
Dr. Johnson is the Charles E. Putman University Professor of Radiology, Professor
of Physics, and Biomedical Engineering, and Director of the Duke Center for In Vivo
Microscopy (CIVM). The CIVM is an NIH/NIBIB national Biomedical Technology Resource
Center with a mission to develop novel technologies for preclinical imaging (basic
sciences) and apply the technologies to critical biomedical questions. Dr. Johnson
was one of the first researchers to bring Paul Lauterbur's vision of magnetic resona
Alphabetical list of authors with Scholars@Duke profiles.

Articles written by Duke faculty are made available through the campus open access policy. For more information see: Duke Open Access Policy
Rights for Collection: Scholarly Articles
Works are deposited here by their authors, and represent their research and opinions, not that of Duke University. Some materials and descriptions may include offensive content. More info