title: 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.
authors: Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, North Carolina 27710.
authors: Jana Schaich
authors: JS
authors: Borg
authors: Department of Neurobiology, Duke University Medical Center, Durham, North Carolina 27710 ; Center for Cognitive Neuroscience, Duke University Medical Center, Durham, North Carolina 27710.
authors: Mai-Anh
authors: MA
authors: Vu
authors: Department of Radiology, Duke University Medical Center, Durham, North Carolina 27710 ; Department of Biomedical Engineering, Duke University Medical Center, Durham, North Carolina 27710 ; Department of Medical Physics, Duke University Medical Center, Durham, North Carolina 27710.
authors: Cristian
authors: C
authors: Badea
authors: Department of Radiology, Duke University Medical Center, Durham, North Carolina 27710.
authors: Alexandra
authors: A
authors: Badea
authors: Department of Radiology, Duke University Medical Center, Durham, North Carolina 27710 ; Department of Biomedical Engineering, Duke University Medical Center, Durham, North Carolina 27710 ; Department of Medical Physics, Duke University Medical Center, Durham, North Carolina 27710 ; Department of Physics, Duke University Medical Center, Durham, North Carolina 27710.
authors: G Allan
authors: GA
authors: Johnson
authors: Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, North Carolina 27710 ; Department of Neurobiology, Duke University Medical Center, Durham, North Carolina 27710 ; Department of Biomedical Engineering, Duke University Medical Center, Durham, North Carolina 27710 ; Center for Neuroengineering, Duke University Medical Center, Durham, North Carolina 27710.
authors: Kafui
authors: K
authors: Dzirasa