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2 Janelia Publications

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    05/23/19 | Computational methods for stitching, alignment, and artifact correction of serial section data.
    Saalfeld S
    Methods in Cell Biology;152:261 - 276. doi: 10.1016/bs.mcb.2019.04.007

    Imaging large samples at the resolution offered by electron microscopy is typically achieved by sequentially recording overlapping tiles that are later combined to seamless mosaics. Mosaics of serial sections are aligned to reconstruct three-dimensional volumes. To achieve this, image distortions and artifacts as introduced during sample preparation or imaging need to be removed.

    In this chapter, we will discuss typical sources of artifacts and distortion, and we will learn how to use the open source software TrakEM2 to correct them.

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    01/18/19 | Cortical column and whole-brain imaging with molecular contrast and nanoscale resolution.
    Gao R, Asano SM, Upadhyayula S, Pisarev I, Milkie DE, Liu T, Singh V, Graves AR, Huynh GH, Zhao Y, Bogovic JA, Colonell J, Ott CM, Zugates CT, Tappan S, Rodriguez A, Mosaliganti KR, Sheu S, Pasolli HA, et al
    Science (New York, N.Y.). 2019 Jan 18;363(6424):eaau8302. doi: 10.1126/science.aau8302

    Optical and electron microscopy have made tremendous inroads toward understanding the complexity of the brain. However, optical microscopy offers insufficient resolution to reveal subcellular details, and electron microscopy lacks the throughput and molecular contrast to visualize specific molecular constituents over millimeter-scale or larger dimensions. We combined expansion microscopy and lattice light-sheet microscopy to image the nanoscale spatial relationships between proteins across the thickness of the mouse cortex or the entire Drosophila brain. These included synaptic proteins at dendritic spines, myelination along axons, and presynaptic densities at dopaminergic neurons in every fly brain region. The technology should enable statistically rich, large-scale studies of neural development, sexual dimorphism, degree of stereotypy, and structural correlations to behavior or neural activity, all with molecular contrast.

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