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55 Publications

Showing 31-40 of 55 results
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    Hess LabFetter LabFlyEM
    02/16/15 | Ultrastructurally smooth thick partitioning and volume stitching for large-scale connectomics.
    Hayworth KJ, Xu CS, Lu Z, Knott GW, Fetter RD, Tapia JC, Lichtman JW, Hess HF
    Nature Methods. 2015 Feb 16;12(4):319-22. doi: 10.1038/nmeth.3292

    Focused-ion-beam scanning electron microscopy (FIB-SEM) has become an essential tool for studying neural tissue at resolutions below 10 nm × 10 nm × 10 nm, producing data sets optimized for automatic connectome tracing. We present a technical advance, ultrathick sectioning, which reliably subdivides embedded tissue samples into chunks (20 μm thick) optimally sized and mounted for efficient, parallel FIB-SEM imaging. These chunks are imaged separately and then 'volume stitched' back together, producing a final three-dimensional data set suitable for connectome tracing.

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    02/01/15 | Connectome of the fly visual circuitry.
    Takemura S
    Microscopy. 2015 Feb;64(1):37-44. doi: 10.1093/jmicro/dfu102

    Recent powerful tools for reconstructing connectomes using electron microscopy (EM) have made outstanding contributions to the field of neuroscience. As a prime example, the detection of visual motion is a classic problem of neural computation, yet our understanding of the exact mechanism has been frustrated by our incomplete knowledge of the relevant neurons and synapses. Recent connectomic studies have successfully identified the concrete neuronal circuit in the fly's visual system that computes the motion signals. This identification was greatly aided by the comprehensiveness of the EM reconstruction. Compared with light microscopy, which gives estimated connections from arbor overlap, EM gives unequivocal connections with precise synaptic counts. This paper reviews the recent study of connectomics in a brain of the fruit fly Drosophila and highlights how connectomes can provide a foundation for understanding the mechanism of neuronal functions by identifying the underlying neural circuits.

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    01/08/15 | Protecting integrated circuits from piracy with test-aware logic locking.
    Plaza SM, Markov IL
    IEEE/ACM International Conference on Computer-Aided Design, Digest of Technical Papers, ICCAD. 2015-01-08:262-269. doi: 10.1109/ICCAD.2014.7001361

    The increasing IC manufacturing cost encourages a business model where design houses outsource IC fabrication to remote foundries. Despite cost savings, this model exposes design houses to IC piracy as remote foundries can manufacture in excess to sell on the black market. Recent efforts in digital hardware security aim to thwart piracy by using XOR-based chip locking, cryptography, and active metering. To counter direct attacks and lower the exposure of unlocked circuits to the foundry, we introduce a multiplexor-based locking strategy that preserves test response allowing IC testing by an untrusted party before activation. We demonstrate a simple yet effective attack against a locked circuit that does not preserve test response, and validate the effectiveness of our locking strategy on IWLS 2005 benchmarks.

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    12/28/14 | Neural computation for rehabilitation.
    Hu X, Wang Y, Zhao T, Gunduz A
    Biomed Research International. 2014;2014:603985. doi: 10.1155/2014/603985
    11/03/14 | Protecting integrated circuits from piracy with test-aware logic locking.
    Plaza SM, Markov IL
    ICCAD '14 Proceedings of the 2014 IEEE/ACM International Conference on Computer-Aided Design. 2014 Nov 03:262-269. doi: 10.1109/ICCAD.2014.7001361

    The increasing IC manufacturing cost encourages a business model where design houses outsource IC fabrication to remote foundries. Despite cost savings, this model exposes design houses to IC piracy as remote foundries can manufacture in excess to sell on the black market. Recent efforts in digital hardware security aim to thwart piracy by using XOR-based chip locking, cryptography, and active metering. To counter direct attacks and lower the exposure of unlocked circuits to the foundry, we introduce a multiplexor-based locking strategy that preserves test response allowing IC testing by an untrusted party before activation. We demonstrate a simple yet effective attack against a locked circuit that does not preserve test response, and validate the effectiveness of our locking strategy on IWLS 2005 benchmarks.

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    09/14/14 | Small sample learning of superpixel classifiers for EM segmentation.
    Parag T, Plaza S, Scheffer L
    Medical Image Computing and Computer-Assisted Intervention. 2014;17(Pt 1):389-97

    Pixel and superpixel classifiers have become essential tools for EM segmentation algorithms. Training these classifiers remains a major bottleneck primarily due to the requirement of completely annotating the dataset which is tedious, error-prone and costly. In this paper, we propose an interactive learning scheme for the superpixel classifier for EM segmentation. Our algorithm is 'active semi-supervised' because it requests the labels of a small number of examples from user and applies label propagation technique to generate these queries. Using only a small set (< 20%) of all datapoints, the proposed algorithm consistently generates a classifier almost as accurate as that estimated from a complete groundtruth. We provide segmentation results on multiple datasets to show the strength of these classifiers.

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    09/05/14 | Annotating synapses in large EM datasets.
    Plaza SM, Parag T, Huang G, Olbris DJ, Saunders MA, Rivlin PK
    arXiv. 2014 Sep 5:arXiv:1409.1801 [q-bio.QM]

    Reconstructing neuronal circuits at the level of synapses is a central problem in neuroscience and becoming a focus of the emerging field of connectomics. To date, electron microscopy (EM) is the most proven technique for identifying and quantifying synaptic connections. As advances in EM make acquiring larger datasets possible, subsequent manual synapse identification ({\em i.e.}, proofreading) for deciphering a connectome becomes a major time bottleneck. Here we introduce a large-scale, high-throughput, and semi-automated methodology to efficiently identify synapses. We successfully applied our methodology to the Drosophila medulla optic lobe, annotating many more synapses than previous connectome efforts. Our approaches are extensible and will make the often complicated process of synapse identification accessible to a wider-community of potential proofreaders.

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    09/05/14 | Automatic neuron type identification by neurite localization in the Drosophila medulla.
    Plaza SM, Zhao T
    arXiv. 2014 Sep 5:arXiv:1409.1892 [q-bio.NC]

    Mapping the connectivity of neurons in the brain (i.e., connectomics) is a challenging problem due to both the number of connections in even the smallest organisms and the nanometer resolution required to resolve them. Because of this, previous connectomes contain only hundreds of neurons, such as in the C.elegans connectome. Recent technological advances will unlock the mysteries of increasingly large connectomes (or partial connectomes). However, the value of these maps is limited by our ability to reason with this data and understand any underlying motifs. To aid connectome analysis, we introduce algorithms to cluster similarly-shaped neurons, where 3D neuronal shapes are represented as skeletons. In particular, we propose a novel location-sensitive clustering algorithm. We show clustering results on neurons reconstructed from the Drosophila medulla that show high-accuracy.

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    09/05/14 | Identifying synapses using deep and wide multiscale recursive networks.
    Huang G, Plaza SM
    arXiv. 2014 Sep 5:arXiv:1409.1789 [cs.CV]

    In this work, we propose a learning framework for identifying synapses using a deep and wide multi-scale recursive (DAWMR) network, previously considered in image segmentation applications. We apply this approach on electron microscopy data from invertebrate fly brain tissue. By learning features directly from the data, we are able to achieve considerable improvements over existing techniques that rely on a small set of hand-designed features. We show that this system can reduce the amount of manual annotation required, in both acquisition of training data as well as verification of inferred detections.

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    09/03/14 | Focused proofreading: efficiently extracting connectomes from segmented EM images.
    Plaza SM
    arXiv. 2014 Sep 3:arXiv:1409.1199 [q-bio.QM]

    Pixel and superpixel classifiers have become essential tools for EM segmentation algorithms. Training these classifiers remains a major bottleneck primarily due to the requirement of completely annotating the dataset which is tedious, error-prone and costly. In this paper, we propose an interactive learning scheme for the superpixel classifier for EM segmentation. Our algorithm is "active semi-supervised" because it requests the labels of a small number of examples from user and applies label propagation technique to generate these queries. Using only a small set (<20%) of all datapoints, the proposed algorithm consistently generates a classifier almost as accurate as that estimated from a complete groundtruth. We provide segmentation results on multiple datasets to show the strength of these classifiers.

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