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139 Publications

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    01/28/08 | A rate-efficient approach for establishing visual correspondences via distributed source coding.
    Yeo C, Ahammad P, Ramchandran K
    SPIE Visual Communications and Image Processing. 2008 Jan 28:

    We consider the problem of communicating compact descriptors for the purpose of establishing visual correspondences between two cameras operating under rate constraints. Establishing visual correspondences is a critical step before other tasks such as camera calibration or object recognition can be performed in a network of cameras. We verify that descriptors of regions which are in correspondence are highly correlated, and propose the use of distributed source coding to reduce the bandwidth needed for transmitting descriptors required to establish correspondence. Our experiments demonstrate that the proposed scheme is able to provide compression gains of 57% with minimal loss in the number of correctly established correspondences compared to a scheme that communicates the entire image of the scene losslessly in compressed form. Over a wide range of rates, the proposed scheme also provides superior performance when compared to simply transmitting all the feature descriptors.

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    Tjian Lab
    01/18/08 | Structural changes in TAF4b-TFIID correlate with promoter selectivity.
    Liu W, Coleman RA, Grob P, King DS, Florens L, Washburn MP, Geles KG, Yang JL, Ramey V, Nogales E, Tjian R
    Molecular Cell. 2008 Jan 18;29(1):81-91. doi: 10.1073/pnas.1100640108

    Proper ovarian development requires the cell type-specific transcription factor TAF4b, a subunit of the core promoter recognition complex TFIID. We present the 35 A structure of a cell type-specific core promoter recognition complex containing TAF4b and TAF4 (4b/4-IID), which is responsible for directing transcriptional synergy between c-Jun and Sp1 at a TAF4b target promoter. As a first step toward correlating potential structure/function relationships of the prototypic TFIID versus 4b/4-IID, we have compared their 3D structures by electron microscopy and single-particle reconstruction. These studies reveal that TAF4b incorporation into TFIID induces an open conformation at the lobe involved in TFIIA and putative activator interactions. Importantly, this open conformation correlates with differential activator-dependent transcription and promoter recognition by 4b/4-IID. By combining functional and structural analysis, we find that distinct localized structural changes in a megadalton macromolecular assembly can significantly alter its activity and lead to a TAF4b-induced reprogramming of promoter specificity.

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    01/15/08 | Straightening caenorhabditis elegans images.
    Peng H, Long F, Liu X, Kim SK, Myers EW
    Bioinformatics. 2008 Jan 15;24:234-42. doi: 10.1093/bioinformatics/btm569

    MOTIVATION: Caenorhabditis elegans, a roundworm found in soil, is a widely studied model organism with about 1000 cells in the adult. Producing high-resolution fluorescence images of C.elegans to reveal biological insights is becoming routine, motivating the development of advanced computational tools for analyzing the resulting image stacks. For example, worm bodies usually curve significantly in images. Thus one must ’straighten’ the worms if they are to be compared under a canonical coordinate system. RESULTS: We develop a worm straightening algorithm (WSA) that restacks cutting planes orthogonal to a ’backbone’ that models the anterior-posterior axis of the worm. We formulate the backbone as a parametric cubic spline defined by a series of control points. We develop two methods for automatically determining the locations of the control points. Our experimental methods show that our approaches effectively straighten both 2D and 3D worm images.

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    Svoboda Lab
    01/03/08 | Sparse optical microstimulation in barrel cortex drives learned behaviour in freely moving mice.
    Huber D, Petreanu L, Ghitani N, Ranade S, Hromádka T, Mainen Z, Svoboda K
    Nature. 2008 Jan 3;451(7174):61-4. doi: 10.1038/nature06445

    Electrical microstimulation can establish causal links between the activity of groups of neurons and perceptual and cognitive functions. However, the number and identities of neurons microstimulated, as well as the number of action potentials evoked, are difficult to ascertain. To address these issues we introduced the light-gated algal channel channelrhodopsin-2 (ChR2) specifically into a small fraction of layer 2/3 neurons of the mouse primary somatosensory cortex. ChR2 photostimulation in vivo reliably generated stimulus-locked action potentials at frequencies up to 50 Hz. Here we show that naive mice readily learned to detect brief trains of action potentials (five light pulses, 1 ms, 20 Hz). After training, mice could detect a photostimulus firing a single action potential in approximately 300 neurons. Even fewer neurons (approximately 60) were required for longer stimuli (five action potentials, 250 ms). Our results show that perceptual decisions and learning can be driven by extremely brief epochs of cortical activity in a sparse subset of supragranular cortical pyramidal neurons.

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    01/02/08 | Universal memory mechanism for familiarity recognition and identification.
    Yakovlev V, Amit DJ, Romani S, Hochstein S
    The Journal of Neuroscience : The Official Journal of the Society for Neuroscience. 2008 Jan 2;28(1):239-48. doi: 10.1523/JNEUROSCI.4799-07.2008

    Macaque monkeys were tested on a delayed-match-to-multiple-sample task, with either a limited set of well trained images (in randomized sequence) or with never-before-seen images. They performed much better with novel images. False positives were mostly limited to catch-trial image repetitions from the preceding trial. This result implies extremely effective one-shot learning, resembling Standing's finding that people detect familiarity for 10,000 once-seen pictures (with 80% accuracy) (Standing, 1973). Familiarity memory may differ essentially from identification, which embeds and generates contextual information. When encountering another person, we can say immediately whether his or her face is familiar. However, it may be difficult for us to identify the same person. To accompany the psychophysical findings, we present a generic neural network model reproducing these behaviors, based on the same conservative Hebbian synaptic plasticity that generates delay activity identification memory. Familiarity becomes the first step toward establishing identification. Adding an inter-trial reset mechanism limits false positives for previous-trial images. The model, unlike previous proposals, relates repetition-recognition with enhanced neural activity, as recently observed experimentally in 92% of differential cells in prefrontal cortex, an area directly involved in familiarity recognition. There may be an essential functional difference between enhanced responses to novel versus to familiar images: The maximal signal from temporal cortex is for novel stimuli, facilitating additional sensory processing of newly acquired stimuli. The maximal signal for familiar stimuli arising in prefrontal cortex facilitates the formation of selective delay activity, as well as additional consolidation of the memory of the image in an upstream cortical module.

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    01/01/08 | A critical role for N-WASp in cell migration during central nervous system development.
    Jin F, Bharioke A, Zhang J, Kuhlmann T, Georgiou J, Lommel S, Siminovitch K
    International Journal of Developmental Neuroscience. 2008;26:413
    01/01/08 | Automatic Segmentation of the Pelvic Bones from CT Data Based on a Statistical Shape Model
    Kainmueller D, Seim H, Heller M, Lamecker H, Zachow S, Hege H

    We present an algorithm for automatic segmentation of the human pelvic bones from CT datasets that is based on the application of a statistical shape model. The proposed method is divided into three steps: 1) The averaged shape of the pelvis model is initially placed within the CT data using the Generalized Hough Transform, 2) the statistical shape model is then adapted to the image data by a transformation and variation of its shape modes, and 3) a final free-form deformation step based on optimal graph searching is applied to overcome the restrictive character of the statistical shape representation. We thoroughly evaluated the method on 50 manually segmented CT datasets by performing a leave-one-out study. The Generalized Hough Transform proved to be a reliable method for an automatic initial placement of the shape model within the CT data. Compared to the manual gold standard segmentations, our automatic segmentation approach produced an average surface distance of 1.2 ± 0.3mm after the adaptation of the statistical shape model, which could be reduced to 0.7±0.3mm using a final free-form deformation step. Together with an average segmentation time of less than 5 minutes, the results of our study indicate that our method meets the requirements of clinical routine.

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    01/01/08 | CITRIC: A Low-bandwidth wireless camera network platform.
    Chen P, Ahammad P
    ACM/IEEE International Conference on Distributed Smart Cameras:2008

    In this paper, we propose and demonstrate a novel wireless camera network system, called CITRIC. The core component of this system is a new hardware platform that integrates a camera, a frequency-scalable (up to 624 MHz) CPU, 16MB FLASH, and 64MB RAM onto a single device. The device then connects with a standard sensor network mote to form a camera mote. The design enables in-network processing of images to reduce communication requirements, which has traditionally been high in existing camera networks with centralized processing. We also propose a back-end client/server architecture to provide a user interface to the system and support further centralized processing for higher-level applications. Our camera mote enables a wider variety of distributed pattern recognition applications than traditional platforms because it provides more computing power and tighter integration of physical components while still consuming relatively little power. Furthermore, the mote easily integrates with existing low-bandwidth sensor networks because it can communicate over the IEEE 802.15.4 protocol with other sensor network platforms. We demonstrate our system on three applications: image compression, target tracking, and camera localization.

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    01/01/08 | Even illumination in total internal reflection fluorescence microscopy using laser light.
    Fiolka R, Belyaev Y, Ewers H, Stemmer A
    Microscopy Research and Technique. 2008 Jan;71(1):45-50. doi: 10.1002/jemt.20527

    In modern fluorescence microscopy, lasers are a widely used source of light, both for imaging in total internal reflection and epi-illumination modes. In wide-field imaging, scattering of highly coherent laser light due to imperfections in the light path typically leads to nonuniform illumination of the specimen, compromising image analysis. We report the design and construction of an objective-launch total internal reflection fluorescence microscopy system with excellent evenness of specimen illumination achieved by azimuthal rotation of the incoming illuminating laser beam. The system allows quick and precise changes of the incidence angle of the laser beam and thus can also be used in an epifluorescence mode.

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    Looger Lab
    01/01/08 | Genetically encoded fluorescent sensors for studying healthy and diseased nervous systems.
    Tian L, Looger LL
    Drug Discovery Today. Disease Models. 2008;5(1):27-35. doi: 10.1016/j.ddmod.2008.07.003

    Neurons and glia are functionally organized into circuits and higher-order structures via synaptic connectivity, well-orchestrated molecular signaling, and activity-dependent refinement. Such organization allows the precise information processing required for complex behaviors. Disruption of nervous systems by genetic deficiency or events such as trauma or environmental exposure may produce a diseased state in which certain aspects of inter-neuron signaling are impaired. Optical imaging techniques allow the direct visualization of individual neurons in a circuit environment. Imaging probes specific for given biomolecules may help elucidate their contribution to proper circuit function. Genetically encoded sensors can visualize trafficking of particular molecules in defined neuronal populations, non-invasively in intact brain or reduced preparations. Sensor analysis in healthy and diseased brains may reveal important differences and shed light on the development and progression of nervous system disorders. We review the field of genetically encoded sensors for molecules and cellular events, and their potential applicability to the study of nervous system disease.

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