TY - JOUR T1 - Localization of metal electrodes in the intact rat brain using registration of 3-D micro-computed tomography images to a magnetic resonance histology atlas JF - eneuro JO - eneuro DO - 10.1523/ENEURO.0017-15.2015 SP - ENEURO.0017-15.2015 AU - Jana Schaich Borg AU - Mai-Anh Vu AU - Cristian Badea AU - Alexandra Badea AU - G. Allan Johnson AU - Kafui Dzirasa Y1 - 2015/07/02 UR - http://www.eneuro.org/content/early/2015/07/02/ENEURO.0017-15.2015.abstract N2 - 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.Significance Statement: The digital imaging technique we present here allows unparalleled 3-D visualization of the anatomical location of large numbers of electrodes implanted deep in the rodent brain. The anatomical location of each electrode can be determined quickly without removing the electrodes from the brain, can be observed from many different angles of view, and can be automated. These features offer substantial improvements over currently available histological methods of electrode location verification. ER -