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2432 Publications

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    01/01/11 | High resolution segmentation of neuronal tissues from low depth-resolution EM imagery.
    Glasner D, Hu T, Nunez-Iglesias J, Scheffer L, Xu C, Hess H, Fetter R, Chklovskii D, Basri R
    8th International Conference of Energy Minimization Methods in Computer Vision and Pattern Recognition Energy Minimization Methods in Computer Vision and Pattern Recognition. 2011;6819:261-72

    The challenge of recovering the topology of massive neuronal circuits can potentially be met by high throughput Electron Microscopy (EM) imagery. Segmenting a 3-dimensional stack of EM images into the individual neurons is difficult, due to the low depth-resolution in existing high-throughput EM technology, such as serial section Transmission EM (ssTEM). In this paper we propose methods for detecting the high resolution locations of membranes from low depth-resolution images. We approach this problem using both a method that learns a discriminative, over-complete dictionary and a kernel SVM. We test this approach on tomographic sections produced in simulations from high resolution Focused Ion Beam (FIB) images and on low depth-resolution images acquired with ssTEM and evaluate our results by comparing it to manual labeling of this data.

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    Looger Lab
    06/01/12 | Imaging neural activity with genetically encoded calcium indicator.
    Tian L, Hires A, Looger LL
    Cold Spring Harbor Protocols. 2012 Jun 1;2012(6):647-56

    Genetically encoded calcium indicators (GECIs), which are based on chimeric fluorescent proteins, can be used to monitor calcium transients in living cells and organisms. Because they are encoded by DNA, GECIs can be delivered to the intact brain noninvasively and targeted to defined populations of neurons and specific subcellular compartments for long-term, repeated measurements in vivo. GECIs have improved iteratively and are becoming useful for imaging neural activity in vivo. Here we summarize extrinsic and intrinsic factors that influence a GECI's performance and provides guidelines for selecting the appropriate GECI for a given application. We also review recent progress in GECI design, optimization, and standardized testing protocols.

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    Dudman LabSvoboda Lab
    01/01/11 | Inputs to the dorsal striatum of the mouse reflect the parallel circuit architecture of the forebrain.
    Pan WX, Mao T, Dudman JT
    Frontiers in Neuroanatomy. 2011;4:147. doi: 10.3389/fnana.2010.00147

    The basal ganglia play a critical role in the regulation of voluntary action in vertebrates. Our understanding of the function of the basal ganglia relies heavily upon anatomical information, but continued progress will require an understanding of the specific functional roles played by diverse cell types and their connectivity. An increasing number of mouse lines allow extensive identification, characterization, and manipulation of specified cell types in the basal ganglia. Despite the promise of genetically modified mice for elucidating the functional roles of diverse cell types, there is relatively little anatomical data obtained directly in the mouse. Here we have characterized the retrograde labeling obtained from a series of tracer injections throughout the dorsal striatum of adult mice. We found systematic variations in input along both the medial-lateral and anterior-posterior neuraxes in close agreement with canonical features of basal ganglia anatomy in the rat. In addition to the canonical features we have provided experimental support for the importance of non-canonical inputs to the striatum from the raphe nuclei and the amygdala. To look for organization at a finer scale we have analyzed the correlation structure of labeling intensity across our entire dataset. Using this analysis we found substantial local heterogeneity within the large-scale order. From this analysis we conclude that individual striatal sites receive varied combinations of cortical and thalamic input from multiple functional areas, consistent with some earlier studies in the rat that have suggested the presence of a combinatorial map.

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    01/01/11 | Learning to agglomerate superpixel hierarchies.
    Jain V, Turaga S, Briggman K, Helmstaedter MN, Denk W, Seung S
    Neural Information Processing Systems. 2011;24:648-56

    An agglomerative clustering algorithm merges the most similar pair of clusters at every iteration. The function that evaluates similarity is traditionally handdesigned, but there has been recent interest in supervised or semisupervised settings in which ground-truth clustered data is available for training. Here we show how to train a similarity function by regarding it as the action-value function of a reinforcement learning problem. We apply this general method to segment images by clustering superpixels, an application that we call Learning to Agglomerate Superpixel Hierarchies (LASH). When applied to a challenging dataset of brain images from serial electron microscopy, LASH dramatically improved segmentation accuracy when clustering supervoxels generated by state of the boundary detection algorithms. The naive strategy of directly training only supervoxel similarities and applying single linkage clustering produced less improvement.

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    12/27/10 | Orphan nuclear receptors control neuronal remodeling during fly metamorphosis.
    Tzumin Lee , Takeshi Awasaki
    Nature Neuroscience. 2010 Dec 27;14:6-7. doi: 10.1038/nn0111-6

    News & Views | Published: 27 December 2010

    Orphan nuclear receptors control neuronal remodeling during fly metamorphosis

    Nature Neuroscience volume 14, pages 6–7 (2011) | Download Citation

    Pruning of excess branches is essential for the maturation of developing neuronal circuits. Cross-talk between TGF-β signaling and two antagonistic orphan nuclear receptors governs the pruning of larval γ neurons in the Drosophila pupa.

    Neural circuits are remodeled as the brain matures or acquires new functions. Such developmental remodeling involves complex cellular changes that are tightly regulated in space and time. During metamorphosis of holometabolous insect brains, most larval functional neurons are rewired into the adult circuitry, and study of these processes has been particularly fruitful for the elucidation of the mechanisms that underlie neuron remodeling1. In metamorphosing Drosophila, nuclear signaling of the steroid hormone receptor ecdysone receptor B1 isoform (EcR-B1) cell-autonomously orchestrates neuron remodeling. Only neurons destined to remodel upregulate EcR-B1 expression before a crucial pre-pupal ecdysone pulse2. It is therefore necessary to determine the mechanisms that pattern EcR-B1 expression to understand how developmental neuronal remodeling is programmed in Drosophila.

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    01/01/11 | Probing tension and dynamics in actomyosin mediated cell shape change.
    Higgins CD, Tulu US, Gao L, Betzig E, Kiehart DP, Goldstein B
    Molecular Biology of the Cell. 2011;22:
    01/01/11 | Pupil-segmentation-based adaptive optics for microscopy.
    Ji N, Milkie DE, Betzig E
    Proceedings of SPIE. 2011;7931:79310I. doi: 10.1117/12.876398

    Inhomogeneous optical properties of biological samples make it difficult to obtain diffraction-limited resolution in depth. Correcting the sample-induced optical aberrations needs adaptive optics (AO). However, the direct wavefront-sensing approach commonly used in astronomy is not suitable for most biological samples due to their strong scattering of light. We developed an image-based AO approach that is insensitive to sample scattering. By comparing images of the sample taken with different segments of the pupil illuminated, local tilt in the wavefront is measured from image shift. The aberrated wavefront is then obtained either by measuring the local phase directly using interference or with phase reconstruction algorithms similar to those used in astronomical AO. We implemented this pupil-segmentation-based approach in a two-photon fluorescence microscope and demonstrated that diffraction-limited resolution can be recovered from nonbiological and biological samples.

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    Eddy/Rivas Lab
    01/01/11 | Rfam: Wikipedia, clans and the "decimal" release.
    Gardner PP, Daub J, Tate J, Moore BL, Osuch IH, Griffiths-Jones S, Finn RD, Nawrocki EP, Kolbe DL, Eddy SR, Bateman A
    Nucleic Acids Research. 2011 Jan;39(Database issue):D141-5. doi: 10.1093/nar/gkq1129

    The Rfam database aims to catalogue non-coding RNAs through the use of sequence alignments and statistical profile models known as covariance models. In this contribution, we discuss the pros and cons of using the online encyclopedia, Wikipedia, as a source of community-derived annotation. We discuss the addition of groupings of related RNA families into clans and new developments to the website. Rfam is available on the Web at http://rfam.sanger.ac.uk.

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    01/01/11 | Studying sensorimotor processing with physiology in behaving Drosophila.
    Seelig JD, Jayaraman V
    International Review of Neurobiology. 2011;99:169-89. doi: 10.1016/B978-0-12-387003-2.00007-0

    The neural underpinnings of sensorimotor integration are best studied in the context of well-characterized behavior. A rich trove of Drosophila behavioral genetics research offers a variety of well-studied behaviors and candidate brain regions that can form the bases of such studies. The development of tools to perform in vivo physiology from the Drosophila brain has made it possible to monitor activity in defined neurons in response to sensory stimuli. More recently still, it has become possible to perform recordings from identified neurons in the brain of head-fixed flies during walking or flight behaviors. In this chapter, we discuss how experiments that simultaneously monitor behavior and physiology in Drosophila can be combined with other techniques to produce testable models of sensorimotor circuit function.

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    01/01/11 | Synthesis and utility of fluorogenic acetoxymethyl ethers.
    Lavis LD, Chao T, Raines RT
    Chemical Science. 2011 Jan 1;2(3):521-30. doi: 10.1039/C0SC00466A

    Phenolic fluorophores such as fluorescein, Tokyo Green, resorufin, and their derivatives are workhorses of biological science. Acylating the phenolic hydroxyl group(s) in these fluorophores masks their fluorescence. The ensuing ester is a substrate for cellular esterases, which can restore fluorescence. These esters are, however, notoriously unstable to hydrolysis, severely compromising their utility. The acetoxymethyl (AM) group is an esterase-sensitive motif that can mask polar functionalities in small molecules. Here, we report on the use of AM ether groups to mask phenolic fluorophores. The resulting profluorophores have a desirable combination of low background fluorescence, high chemical stability, and high enzymatic reactivity, both in vitro and in cellulo. These simple phenyl ether-based profluorophores could supplement or supplant the use of phenyl esters for imaging biochemical and biological systems.

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