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Ashburn, VA, United States

Cui M.,HHMI Janelia Research Campus
Frontiers in Optics, FiO 2014 | Year: 2014

We developed a super-penetration microscope that effectively compensates the wavefront distortion encountered in scattering biological systems. We report high-resolution in vivo imaging of mouse cerebral cortex at large depth and noninvasive imaging through intact mouse skull.

Dunst S.,Max Planck Institute of Molecular Cell Biology and Genetics | Kazimiers T.,Max Planck Institute of Molecular Cell Biology and Genetics | Kazimiers T.,HHMI Janelia Research Campus | von Zadow F.,Max Planck Institute of Molecular Cell Biology and Genetics | And 10 more authors.
Developmental Cell | Year: 2015

Membrane trafficking is key to the cell biological mechanisms underlying development. Rab GTPases control specific membrane compartments, from coresecretory and endocytic machinery to less-well-understood compartments. We tagged all 27 Drosophila Rabs with YFPMYC at their endogenous chromosomal loci, determined their expression and subcellular localization in six tissues comprising 23 cell types, and provide this data in an annotated, searchable image database. We demonstrate the utility of these lines for controlled knockdown and show that similar subcellular localization can predict redundant functions. We exploit this comprehensive resource to ask whether a common Rab compartment architecture underlies epithelial polarity. Strikingly, no single arrangement of Rabs characterizes the five epithelia we examine. Rather, epithelia flexibly polarize Rab distribution, producing membrane trafficking architectures that are tissue- and stage-specific. Thus, the core machinery responsible for epithelial polarization is unlikely to rely on polarized positioning of specific Rab compartments. © 2015 The Authors.

Schmied C.,Max Planck Institute of Molecular Cell Biology and Genetics | Steinbach P.,Max Planck Institute of Molecular Cell Biology and Genetics | Pietzsch T.,Max Planck Institute of Molecular Cell Biology and Genetics | Preibisch S.,Max Planck Institute of Molecular Cell Biology and Genetics | And 3 more authors.
Bioinformatics | Year: 2016

Summary: Selective Plane Illumination Microscopy (SPIM) allows to image developing organisms in 3D at unprecedented temporal resolution over long periods of time. The resulting massive amounts of raw image data requires extensive processing interactively via dedicated graphical user interface (GUI) applications. The consecutive processing steps can be easily automated and the individual time points can be processed independently, which lends itself to trivial parallelization on a high performance computing (HPC) cluster. Here, we introduce an automated workflow for processing large multiview, multichannel, multiillumination time-lapse SPIM data on a single workstation or in parallel on a HPC cluster. The pipeline relies on snakemake to resolve dependencies among consecutive processing steps and can be easily adapted to any cluster environment for processing SPIM data in a fraction of the time required to collect it. Availability and implementation: The code is distributed free and open source under the MIT license http://opensource.org/licenses/MIT. The source code can be downloaded from github: https://github.com/mpicbg-scicomp/snakemake-workflows. Documentation can be found here: http://fiji.sc/Automated-workflow-for-parallel-Multiview-Reconstruction. © 2015 The Author 2015. Published by Oxford University Press.

Dolan M.-J.,University of Cambridge | Dolan M.-J.,HHMI Janelia Research Campus | Huoviala P.,University of Cambridge | Jefferis G.,University of Cambridge
Current Biology | Year: 2015

The same sensory signal can be interpreted differently according to context. A new study in Drosophila uses cell-type-specific tools to identify neural circuits that integrate context during olfactory processing and surprisingly implicates memory-recall neurons. © 2015 Elsevier Ltd.

Dyakova O.,Uppsala University | Lee Y.-J.,Uppsala University | Longden K.D.,HHMI Janelia Research Campus | Kiselev V.G.,Albert Ludwigs University of Freiburg | And 2 more authors.
Nature Communications | Year: 2015

Animal sensory systems are optimally adapted to those features typically encountered in natural surrounds, thus allowing neurons with limited bandwidth to encode challengingly large input ranges. Natural scenes are not random, and peripheral visual systems in vertebrates and insects have evolved to respond efficiently to their typical spatial statistics. The mammalian visual cortex is also tuned to natural spatial statistics, but less is known about coding in higher order neurons in insects. To redress this we here record intracellularly from a higher order visual neuron in the hoverfly. We show that the cSIFE neuron, which is inhibited by stationary images, is maximally inhibited when the slope constant of the amplitude spectrum is close to the mean in natural scenes. The behavioural optomotor response is also strongest to images with naturalistic image statistics. Our results thus reveal a close coupling between the inherent statistics of natural scenes and higher order visual processing in insects. © 2015 Macmillan Publishers Limited.

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