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112 Janelia Publications

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    06/01/12 | Visualization and analysis of 3D microscopic images.
    Long F, Zhou J, Peng H
    PLoS Computational Biology. 2012 Jun;8:e1002519. doi: 10.1371/journal.pcbi.1002519

    In a wide range of biological studies, it is highly desirable to visualize and analyze three-dimensional (3D) microscopic images. In this primer, we first introduce several major methods for visualizing typical 3D images and related multi-scale, multi-time-point, multi-color data sets. Then, we discuss three key categories of image analysis tasks, namely segmentation, registration, and annotation. We demonstrate how to pipeline these visualization and analysis modules using examples of profiling the single-cell gene-expression of C. elegans and constructing a map of stereotyped neurite tracts in a fruit fly brain.

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    Bock Lab
    02/01/12 | Volume electron microscopy for neuronal circuit reconstruction.
    Briggman KL, Bock DD
    Current Opinion in Neurobiology. 2012 Feb;22(1):154-61. doi: 10.1016/j.conb.2011.10.022

    The last decade has seen a rapid increase in the number of tools to acquire volume electron microscopy (EM) data. Several new scanning EM (SEM) imaging methods have emerged, and classical transmission EM (TEM) methods are being scaled up and automated. Here we summarize the new methods for acquiring large EM volumes, and discuss the tradeoffs in terms of resolution, acquisition speed, and reliability. We then assess each method’s applicability to the problem of reconstructing anatomical connectivity between neurons, considering both the current capabilities and future prospects of the method. Finally, we argue that neuronal ’wiring diagrams’ are likely necessary, but not sufficient, to understand the operation of most neuronal circuits: volume EM imaging will likely find its best application in combination with other methods in neuroscience, such as molecular biology, optogenetics, and physiology.

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