Author
Raju Tomer
Other affiliations: Stanford University, Indian Institutes of Technology, European Bioinformatics Institute ...read more
Bio: Raju Tomer is an academic researcher from Columbia University. The author has contributed to research in topics: Light sheet fluorescence microscopy & Microscopy. The author has an hindex of 24, co-authored 40 publications receiving 3887 citations. Previous affiliations of Raju Tomer include Stanford University & Indian Institutes of Technology.
Papers
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TL;DR: Protocols spanning multiple dimensions of the CLARITY workflow are described, ranging from simple, reliable and efficient lipid removal without electrophoretic instrumentation to optimized objectives and integration with light-sheet optics (CLARITY-optimized light- sheet microscopy (COLM)) for accelerating data collection from clarified samples by several orders of magnitude while maintaining or increasing quality and resolution.
Abstract: CLARITY enables the chemical transformation of intact biological tissues into a hydrogel–tissue hybrid. The hybrid samples can be interrogated using light and macromolecular labels, whilst retaining fine structure and native biological molecules.
776 citations
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TL;DR: Two parallel nigrostriatal dopamine neuron subpopulations differing in biophysical properties, input wiring, output wiring to dorsomedial striatum versus dorsolateral striatum (DLS), and natural activity patterns during free behavior are identified.
582 citations
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TL;DR: This work developed one-photon and multiphoton SiMView implementations and recorded cellular dynamics in entire Drosophila melanogaster embryos with 30-s temporal resolution throughout development and performed high-resolution long-term imaging of the developing nervous system and followed neuroblast cell lineages in vivo.
Abstract: Simultaneous multiview light-sheet microscopy using two illumination and two detection arms with one- or two-photon illumination is coupled to a fast data acquisition framework and analysis pipeline for quantitative imaging and tracking of individual cells and the developing nervous system throughout a living fly embryo. A related paper by Krzic et al. is also in this issue.
516 citations
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Medical University of Vienna1, Karolinska Institutet2, Stanford University3, Hungarian Academy of Sciences4, Semmelweis University5, Université catholique de Louvain6, Carl Zeiss AG7, University of Calgary8, Gunma University9, Austrian Academy of Sciences10, Royal Institute of Technology11, University of Kiel12, Yale University13
TL;DR: A catalog of neuronal subclasses provides new understanding of hypothalamic organization and function and distinguished 62 neuronal subtypes producing glutamatergic, dopaminergic or GABAergic markers for synaptic neurotransmission and harboring the ability to engage in task-dependent neurotransmitter switching.
Abstract: The hypothalamus is a brain region rich in functionally segregated neurons. Here Romanov and colleagues use single-cell RNA sequencing to distinguish 62 neuronal subtypes and define their neuropeptide and neurotransmitter makeup. They then show that onecut-3-containing dopamine neurons populate the periventricular area and are wired into the circadian circuitry.
340 citations
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TL;DR: Findings reveal that microRNA evolution and the establishment of tissue identities were closely coupled in bilaterian evolution, and outline a minimum set of cell types and tissues that existed in the protostome–deuterostome ancestor.
Abstract: The spectacular escalation in complexity in early bilaterian evolution correlates with a strong increase in the number of microRNAs. To explore the link between the birth of ancient microRNAs and body plan evolution, we set out to determine the ancient sites of activity of conserved bilaterian microRNA families in a comparative approach. We reason that any specific localization shared between protostomes and deuterostomes (the two major superphyla of bilaterian animals) should probably reflect an ancient specificity of that microRNA in their last common ancestor. Here, we investigate the expression of conserved bilaterian microRNAs in Platynereis dumerilii, a protostome retaining ancestral bilaterian features, in Capitella, another marine annelid, in the sea urchin Strongylocentrotus, a deuterostome, and in sea anemone Nematostella, representing an outgroup to the bilaterians. Our comparative data indicate that the oldest known animal microRNA, miR-100, and the related miR-125 and let-7 were initially active in neurosecretory cells located around the mouth. Other sets of ancient microRNAs were first present in locomotor ciliated cells, specific brain centres, or, more broadly, one of four major organ systems: central nervous system, sensory tissue, musculature and gut. These findings reveal that microRNA evolution and the establishment of tissue identities were closely coupled in bilaterian evolution. Also, they outline a minimum set of cell types and tissues that existed in the protostome-deuterostome ancestor.
290 citations
Cited by
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01 Jan 2006
TL;DR: Probability distributions of linear models for regression and classification are given in this article, along with a discussion of combining models and combining models in the context of machine learning and classification.
Abstract: Probability Distributions.- Linear Models for Regression.- Linear Models for Classification.- Neural Networks.- Kernel Methods.- Sparse Kernel Machines.- Graphical Models.- Mixture Models and EM.- Approximate Inference.- Sampling Methods.- Continuous Latent Variables.- Sequential Data.- Combining Models.
10,141 citations
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TL;DR: RNA sequencing of half a million single cells was used to create a detailed census of cell types in the mouse nervous system and mapped cell types spatially and derived a hierarchical, data-driven taxonomy.
1,735 citations
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Howard Hughes Medical Institute1, Florida State University2, University of the Sciences3, National Institutes of Health4, University of Minnesota5, University of Cambridge6, University of California, San Francisco7, University of Tennessee8, Max Planck Society9, Johns Hopkins University10, Duke University11
TL;DR: A new microscope using ultrathin light sheets derived from two-dimensional optical lattices is developed, demonstrating the performance advantages of lattice light-sheet microscopy compared with previous techniques and highlighted phenomena that, when seen at increased spatiotemporal detail, may hint at previously unknown biological mechanisms.
Abstract: Although fluorescence microscopy provides a crucial window into the physiology of living specimens, many biological processes are too fragile, are too small, or occur too rapidly to see clearly with existing tools. We crafted ultrathin light sheets from two-dimensional optical lattices that allowed us to image three-dimensional (3D) dynamics for hundreds of volumes, often at subsecond intervals, at the diffraction limit and beyond. We applied this to systems spanning four orders of magnitude in space and time, including the diffusion of single transcription factor molecules in stem cell spheroids, the dynamic instability of mitotic microtubules, the immunological synapse, neutrophil motility in a 3D matrix, and embryogenesis in Caenorhabditis elegans and Drosophila melanogaster. The results provide a visceral reminder of the beauty and the complexity of living systems.
1,585 citations
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07 Nov 2014TL;DR: A guide to using some of the recently added advanced μManager features, including hardware synchronization, simultaneous use of multiple cameras, projection of patterned light onto a specimen, live slide mapping, imaging with multi-well plates, particle localization and tracking, and high-speed imaging.
Abstract: μManager is an open-source, cross-platform desktop application, to control a wide variety of motorized microscopes, scientific cameras, stages, illuminators, and other microscope accessories. Since its inception in 2005, μManager has grown to support a wide range of microscopy hardware and is now used by thousands of researchers around the world. The application provides a mature graphical user interface and offers open programming interfaces to facilitate plugins and scripts. Here, we present a guide to using some of the recently added advanced μManager features, including hardware synchronization, simultaneous use of multiple cameras, projection of patterned light onto a specimen, live slide mapping, imaging with multi-well plates, particle localization and tracking, and high-speed imaging.
1,547 citations