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Schalek, Richard

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Schalek

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Richard

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Schalek, Richard
Author's Publications: search.filters.isAuthorOfPublication.622034ca-d6d3-4cb5-ba60-fb7350457610

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    Connectomes across development reveal principles of brain maturation
    (Cold Spring Harbor Laboratory, 2020-04-30) Witvliet, Daniel; Mulcahy, Ben; Mitchell, James; Meirovitch, Yaron; Berger, Daniel; Wu, Yuelong; Liu, Yufang; Koh, Wan Xian; Parvathala, Rajeev; Holmyard, Douglas; Schalek, Richard; Shavit, Nir; Chisholm, Andrew; Lichtman, Jeff; Samuel, Aravi; Zhen, Mei
    From birth to adulthood, an animal’s nervous system changes as its body grows and its behaviours mature. The form and extent of circuit remodelling across the connectome is unknown. We used serial-section electron microscopy to reconstruct the full brain of eight isogenic C. elegans individuals across postnatal stages to learn how it changes with age. The overall geometry of the nervous system is preserved from birth to adulthood. Upon this constant scaffold, substantial changes in chemical synaptic connectivity emerge. Comparing connectomes among individuals reveals substantial connectivity differences that make each brain partly unique. Comparing connectomes across maturation reveals consistent wiring changes between different neurons. These changes alter the strength of existing connections and create new connections. Collective changes in the network alter information processing. Over development, the central decision-making circuitry is maintained whereas sensory and motor pathways substantially remodel. With age, the brain progressively becomes more feedforward and discernibly modular. Developmental connectomics reveals principles that underlie brain maturation.
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    Efficiency of Cathodoluminescence Emission by Nitrogen-Vacancy Color Centers in Nanodiamonds
    (Wiley, 2017-04-18) Zhang, Huiliang; Glenn, David; Schalek, Richard; Lichtman, Jeff; Walsworth, Ronald
    Correlated electron microscopy and cathodoluminescence (CL) imaging using functionalized nanoparticles is a promising nanoscale probe of biological structure and function. Nanodiamonds (NDs) that contain CL‐emitting color centers are particularly well suited for such applications. The intensity of CL emission from NDs is determined by a combination of factors, including particle size, density of color centers, efficiency of energy deposition by electrons passing through the particle, and conversion efficiency from deposited energy to CL emission. This paper reports experiments and numerical simulations that investigate the relative importance of each of these factors in determining CL emission intensity from NDs containing nitrogen‐vacancy (NV) color centers. In particular, it is found that CL can be detected from NV‐doped NDs with dimensions as small as ≈40 nm, although CL emission decreases significantly for smaller NDs.
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    Reconstruction of genetically identified neurons imaged by serial-section electron microscopy
    (eLife Sciences Publications, Ltd, 2016) Joesch, Maximilian; Mankus, David; Yamagata, Masahito; Shahbazi, Ali; Schalek, Richard; Suissa-Peleg, Adi; Meister, Markus; Lichtman, Jeff; Scheirer, Walter J; Sanes, Joshua
    Resolving patterns of synaptic connectivity in neural circuits currently requires serial section electron microscopy. However, complete circuit reconstruction is prohibitively slow and may not be necessary for many purposes such as comparing neuronal structure and connectivity among multiple animals. Here, we present an alternative strategy, targeted reconstruction of specific neuronal types. We used viral vectors to deliver peroxidase derivatives, which catalyze production of an electron-dense tracer, to genetically identify neurons, and developed a protocol that enhances the electron-density of the labeled cells while retaining the quality of the ultrastructure. The high contrast of the marked neurons enabled two innovations that speed data acquisition: targeted high-resolution reimaging of regions selected from rapidly-acquired lower resolution reconstruction, and an unsupervised segmentation algorithm. This pipeline reduces imaging and reconstruction times by two orders of magnitude, facilitating directed inquiry of circuit motifs. DOI: http://dx.doi.org/10.7554/eLife.15015.001
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    Silicon-Vacancy Color Centers in Nanodiamonds: Cathodoluminescence Imaging Markers in the Near Infrared
    (Wiley-Blackwell, 2014) Zhang, Huiliang; Aharonovich, Igor; Glenn, David R.; Schalek, Richard; Magyar, Andrew; Lichtman, Jeff; Hu, Evelyn; Walsworth, Ronald
    Nanodiamonds doped with silicon-vacancy (Si-V) color centers are shown to be a promising candidate for cathodoluminescence (CL) imaging at the nanoscale, providing bright, non-bleaching, narrow-linewidth emission at wavelengths within the near-IR window of biological tissue. CL emission intensity from negative charge-state Si-V centers is greatly enhanced by increasing the nitrogen concentration during nanodiamond growth.
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    Correlative light and electron microscopy using cathodoluminescence from nanoparticles with distinguishable colours
    (Nature Publishing Group, 2012) Glenn, David; Zhang, Huidan; Kasthuri, Narayanan; Schalek, Richard; Lo, P. K.; Trifonov, Alexei; Park, Hongkun; Lichtman, Jeff; Walsworth, Ronald
    Correlative light and electron microscopy promises to combine molecular specificity with nanoscale imaging resolution. However, there are substantial technical challenges including reliable co-registration of optical and electron images, and rapid optical signal degradation under electron beam irradiation. Here, we introduce a new approach to solve these problems: imaging of stable optical cathodoluminescence emitted in a scanning electron microscope by nanoparticles with controllable surface chemistry. We demonstrate well-correlated cathodoluminescence and secondary electron images using three species of semiconductor nanoparticles that contain defects providing stable, spectrally-distinguishable cathodoluminescence. We also demonstrate reliable surface functionalization of the particles. The results pave the way for the use of such nanoparticles for targeted labeling of surfaces to provide nanoscale mapping of molecular composition, indicated by cathodoluminescence colour, simultaneously acquired with structural electron images in a single instrument.