Supporting Material and Data for:
Localization of metal electrodes in the intact rat brain using registration of 3-D micro-computed tomography images to a magnetic resonance histology atlas
Jana Schaich Borg, Mai-Anh Vu, Cristian Badea, Alexandra Badea, G. Allan Johnson, and Kafui Dzirasa
Duke University and Duke University Medical Center, Durham, NC
eNeuro, 2015 Jul-Aug;2(4) pii: e0017. PMCID: PMC4550316
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 trajectory of electrode bundles 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.
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Sample image data for CT and B) are provided, as well as a brain mask. Image data are in NIFTI format and gzipped nifti).
Matlab code is provided to help localize implanted electrodes with respect to the brain, based on registering the CT to the MR atlas image. The code requires an atlas brain mask, provided as well. The main function is called regCT2MR_allSteps.m, and makes use of all subsequent scripts, as well as a few dependencies (NIFTI tools from Jimmy Shen) and strel3d (from Luke Xie) - both available from Matlab central.
While the code is shared under a BSD license and is open for research purposes it is not guaranteed to be fit for any particular, and especially clinical purpose.
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The authors would like to thank James Cook, Center for In Vivo Microscopy, Duke University. We are grateful for support from Duke University Exploratory Research Fund, NIA K01-AG041211, Duke Center for In Vivo Microscopy (NIH/NIBIB P41 EB015897)