Abstract
Simultaneous neural recordings taken from multiple areas of the rodent brain are garnering growing interest because of 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 3D computed 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 “reslicing” the images along different planes of view. Furthermore, 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.
Highlights
A major goal of neuroscience is to understand how spatially distributed neural networks facilitate specific types of behavior (Lewis et al, 2015)
Highlighting one of the advantages of using a 3D magnetic resonance imaging histology (MRH) atlas, when the physical brain slices used for histology were not cut perfectly perpendicular to the anterior–posterior axis, the registered computed tomography (CT) overlaid on the MRH could be “resliced” to match the plane of the histology slice without losing any eNeuro.sfn.org
Measuring electrical activity from electrodes implanted across multiple brain areas simultaneously in awake, behaving rodents holds great potential for uncovering the mechanisms underlying distributed neural networks
Summary
A major goal of neuroscience is to understand how spatially distributed neural networks facilitate specific types of behavior (Lewis et al, 2015). Recordings that use up to 64 microwires spread across up to five brain regions have been reported in rats (Nicolelis et al, 1997; de Araujo et al.,2006; Igarashi et al, 2014; Headley et al, 2015), and up to 64 microwires spread across up to 11 brain regions have been reported in mice (Sigurdsson et al, 2010; Dzirasa et al, 2011). In all of these cases, individual MEAs were implanted into spatially separated brain regions
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