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- I am an interdisciplinary scientist and engineer. My research spans experimental physics, astronomy, and computer sc... moreI am an interdisciplinary scientist and engineer. My research spans experimental physics, astronomy, and computer science with current focus on applications of computer vision and image analysis.edit
This paper describes the near-infrared grism spectrometer and imager (GRIM) designed for use on the Astrophysical Research Consortium telescope. The GRIM system incorporates a wide range of imaging, spectroscopic, and polarimetric... more
This paper describes the near-infrared grism spectrometer and imager (GRIM) designed for use on the Astrophysical Research Consortium telescope. The GRIM system incorporates a wide range of imaging, spectroscopic, and polarimetric capabilities. Attention is given to the mechanical and optical layout of GRIM, the details of the optical design, and the basic components of the remote observing system.
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K BAND PHOTOMETRY OF A COMPLETE SAMPLE OF FIELD GALAXIES WITH SPECTROSCOPIC REDSHIFTS MATTHEW BERSHADY, MARK HERELD, AND RICHARD KRON Department of Astronomy & Astrophysics, University of Chicago, 5640 S. Effis Avenue,... more
K BAND PHOTOMETRY OF A COMPLETE SAMPLE OF FIELD GALAXIES WITH SPECTROSCOPIC REDSHIFTS MATTHEW BERSHADY, MARK HERELD, AND RICHARD KRON Department of Astronomy & Astrophysics, University of Chicago, 5640 S. Effis Avenue, Chicago ...
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Visualization of large-scale simulations running on supercomputers requires ultra-high resolution images to capture important features in the data. In this work, we present a system for streaming ultra-high resolution images from a... more
Visualization of large-scale simulations running on supercomputers requires ultra-high resolution images to capture important features in the data. In this work, we present a system for streaming ultra-high resolution images from a visualization cluster to a remote tiled display at nearly interactive frame rates. vl3, a modular framework for large scale data visualization and analysis, provides the backbone of our implementation. With this system we are able to stream over the network volume renderings of a 20483 voxel dataset at a resolution of 6144×3072 pixels with a frame rate of approximately 3.3 frames per second.
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The SIDGrid architecture provides a framework for distributed annotation, archiving, and analysis of the rapidly growing volume of multimodal data. The framework integrates three main components: an annotation and analysis client, a... more
The SIDGrid architecture provides a framework for distributed annotation, archiving, and analysis of the rapidly growing volume of multimodal data. The framework integrates three main components: an annotation and analysis client, a web-accessible data repository, and a portal to the distributed processing capability of the TeraGrid. The architecture provides both a novel integration of annotation, analysis, and search for multimodal data and a powerful framework for web-based, distributed collaborative annotation and analysis. The flexibility and capabilities of the system have been demonstrated through archiving Talkbank and other spoken discourse and dialogue data and performing joint multimodal analysis of lexical, prosodic, turntaking, and other multimodal factors.
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Computational models of brain tissue provide important insights for understanding pathological behavior within neuronal networks. Validating these models poses difficult challenges due to the number of neurons and synaptic connections in... more
Computational models of brain tissue provide important insights for understanding pathological behavior within neuronal networks. Validating these models poses difficult challenges due to the number of neurons and synaptic connections in even the most modest samples. An important step toward validation is determining connectivity within the biological network so that simulations can be configured to match and then compared directly to the observed behaviors. Cultures of dissociated neurons on multi-electrode arrays provide a flexible experimental platform for the study of fundamental network behaviors. Extracting connectivity from this in vitro setup is challenging because we are able to measure only a relatively small number of neurons. Today, cultures are routinely grown on arrays of microelectrodes, each reporting the activity of several neurons. With these techniques we can distinguish at most hundreds of spiking neurons while cultures comprise thousands of neurons. Even as the number of electrodes increases with gains in technology, it is important to understand how much information about the network connectivity can be discovered with sparse spatial sampling. We describe an approach to searching for repeating patterns in parallel spike train data, the presence of which can inform inferences of causality and connectivity in the network.
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THE STELLAR AND DUST EMISSION FROM NGC 6240 AND M82 AND THE MISAPPLICATION OF ANALOGY HARLEY A. THRONSON, JR. Royal Observatory, Blackford Hill, Edinburgh EH9 311J, Scotland STEVE MAJEWSKI & MARK HERELD Dept. of Astronomy and... more
THE STELLAR AND DUST EMISSION FROM NGC 6240 AND M82 AND THE MISAPPLICATION OF ANALOGY HARLEY A. THRONSON, JR. Royal Observatory, Blackford Hill, Edinburgh EH9 311J, Scotland STEVE MAJEWSKI & MARK HERELD Dept. of Astronomy and Astrophysics, University of Chicago LARA DESCARTES Dept. of Physics, Massachusetts Institute of Technology ABSTRACT We find that the older stellar population in the putative “starburst galaxy” NGC 6240 is sufficiently luminous to contribute a major fraction of the heating of its disrupted, dusty ...
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This paper presents the design and prototyping of hardware and software to address the problem of rapid and reliable 3D digitization of very large collections of pinned insects. Using the collection at the Field Museum of Natural History... more
This paper presents the design and prototyping of hardware and software to address the problem of rapid and reliable 3D digitization of very large collections of pinned insects. Using the collection at the Field Museum of Natural History (FMNH) as a use case, a pipeline to ingest the entire collection of 4.5 million specimens in circa 1-2 years imposes a few second limit on average processing time per specimen. We describe the design and implementation of multi-camera systems capable of rapidly capturing light field imagery for 3D reconstruction of label surfaces and specimen in single snapshots consistent with this time constraint. With imagery captured using these prototype multi-cameras we demonstrate methods under development for 3D reconstruction of pinned insect specimens and for processing text on label surfaces.
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A principal goal of this work is to determine connectivity in cultured neuronal networks as they mature so that we can understand the relationship between connectivity and behavior in biologically generated neuronal net-works. A challenge... more
A principal goal of this work is to determine connectivity in cultured neuronal networks as they mature so that we can understand the relationship between connectivity and behavior in biologically generated neuronal net-works. A challenge of this aim is that we are able to mea-sure only a relatively small number of neurons. In our lab the cultures are grown on a arrays of 60 electrodes. With current techniques we can distinguish at most a handful of spiking neurons while mature cultures comprise more than 10K neurons. At this stage in the work we have col-lected data during development of cultures over a full 30 minutes of sub-millisecond samples. In this paper we present two complementary approaches to the problem. First, we present our results of a brute force search for precisely matched timing differences
Copyright © 2013 Lorenzo L. Pesce et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work... more
Copyright © 2013 Lorenzo L. Pesce et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Our limited understanding of the relationship between the behavior of individual neurons and large neuronal networks is an important limitation in current epilepsy research andmay be one of the main causes of our inadequate ability to treat it. Addressing this problem directly via experiments is impossibly complex; thus, we have been developing and studying medium-large-scale simulations of detailed neuronal networks to guide us. Flexibility in the connection schemas and a complete description of the cortical tissue seem necessary for this purpose. In this paper we examine some of the basic issues encountered in these multiscale simulations.We have determined the detailed behavior of two such simulators on parallel computer systems...
Abstract—We evaluate occurrence of seizure-like activity in computational network models based on the histology of mammalian cortex. In the simulations, seizure onset activity in a network (active patch) is connected to a larger patch of... more
Abstract—We evaluate occurrence of seizure-like activity in computational network models based on the histology of mammalian cortex. In the simulations, seizure onset activity in a network (active patch) is connected to a larger patch of cells (passive patch). The following scenarios were investigated: (1) the active- and passive patches are contiguous with all connectivity intact; (2) active and passive populations are separated (≥1mm interdistance) with long-range connectivity dominating between them. We find that linking the active patch with a passive patch of sufficient excitatory susceptibility reduces pathological network bursting behavior otherwise present in the active patch, even over a separation of several mm. In addition, the balance of excitatory and inhibitory strength in the passive patch plays a crucial role in its ability to restrain network bursting in the active patch: unexpectedly, if the activity in the passive patch is too low, then the active patch can drive ...
Visualization of large-scale simulations running on supercomputers requires ultra-high resolution images to capture important features in the data. In this work, we present a system for streaming ultra-high resolution images from a... more
Visualization of large-scale simulations running on supercomputers requires ultra-high resolution images to capture important features in the data. In this work, we present a system for streaming ultra-high resolution images from a visualization cluster to a remote tiled display at nearly interactive frame rates. vl3, a modular framework for large scale data visualization and analysis, provides the backbone of our implementation. With this system we are able to stream over the network volume renderings of a 20483 voxel dataset at a resolution of 6144×3072 pixels with a frame rate of approximately 3.3 frames per second.
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Since HartreeFock theory often predicts stable negative ions to lie above the analogous neutral +e, there have been legitimate concerns that structural predictions at this level of theory may be of dubious value. To investigate this... more
Since HartreeFock theory often predicts stable negative ions to lie above the analogous neutral +e, there have been legitimate concerns that structural predictions at this level of theory may be of dubious value. To investigate this question, ab initio electronic structure theory has ...
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A search for gravitational radiation from the "millisecond pulsar", PSR 1937+214, using a 40 meter baseline laser interferometric detector is described. Four days of observation yielded 1.2 x 105 seconds of data. Throughout the... more
A search for gravitational radiation from the "millisecond pulsar", PSR 1937+214, using a 40 meter baseline laser interferometric detector is described. Four days of observation yielded 1.2 x 105 seconds of data. Throughout the experiment, the pulsar phase was synthesized to an accuracy of better than one tenth of the pulsar period. A trigger generated from this signal synchronized the data averaging. Narrow band amplitude spectra centered at the pulsar's fundamental electromagnetic pulsation frequency (~642 Hz) and its first harmonic were obtained. The spectra, one for each combination of polarization and center frequency, place 99.7% confidence level limits on the emitted gravitational radiation. In dimensionless strain, h, the rms limits are: 642 Hz "plus" polarization 1.6 x 10-17 " "cross" " 3.1 x 10-17 1294 Hz "plus" polarization 1.1 x 10-17 " "cross" " 1.5 x 10-17 Over the four day observing period, the ...
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Volumetric biological imaging often involves compromising high temporal resolution at the expense of high spatial resolution when popular scanning methods are used to capture 3D information. We introduce an integrated experimental and... more
Volumetric biological imaging often involves compromising high temporal resolution at the expense of high spatial resolution when popular scanning methods are used to capture 3D information. We introduce an integrated experimental and image reconstruction method for capturing dynamic 3D fluorescent extended objects as a series of synchronously measured 3D snapshots taken at the frame rate of the imaging camera. We employ multifocal microscopy (MFM) to simultaneously image at 25 focal planes and process this depth-encoded image to recover the 3D structure of extended objects, such as bacteria, using a sparsity-based reconstruction approach. The combined experimental and computational method produces image quality similar to confocal microscopy in a fraction of the acquisition time. In addition, our computational image reconstruction approach allows a simplified MFM optical design by correcting aberrations using the measured response to point sources. This "compressive" MFM ...
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GPU-based clusters are an attractive option for parallel volume rendering. One of the key issues in parallel volume rendering is load balancing, keeping a balanced workload per node is essential for improving performance. A good number of... more
GPU-based clusters are an attractive option for parallel volume rendering. One of the key issues in parallel volume rendering is load balancing, keeping a balanced workload per node is essential for improving performance. A good number of dynamic load balancing schemes have been proposed throughout the years. However, most of these approaches require runtime dynamic data movement or data duplication. For the large datasets routinely generated by scientific applications, frequent data transfer can be prohibitively expensive. In this work, we propose a static load balancing scheme. By optimizing data placement, a balanced workload can be achieved with minimal or no data movement, therefore improving the rendering speed and user experience.
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Volumetric biological imaging often involves compromising high temporal resolution at the expense of high spatial resolution when popular scanning methods are used to capture 3D information. We introduce an integrated experimental and... more
Volumetric biological imaging often involves compromising high temporal resolution at the expense of high spatial resolution when popular scanning methods are used to capture 3D information. We introduce an integrated experimental and image reconstruction method for capturing dynamic 3D fluorescent extended objects as a series of synchronously measured 3D snapshots taken at the frame rate of the imaging camera. We employ multifocal microscopy (MFM) to simultaneously image at 25 focal planes and process this depth-encoded image to recover the 3D structure of extended objects, such as bacteria, using a sparsity-based reconstruction approach. The combined experimental and computational method produces image quality similar to confocal microscopy in a fraction of the acquisition time. In addition, our computational image reconstruction approach allows a simplified MFM optical design by correcting aberrations using the measured response to point sources. This "compressive" MFM ...
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Digital technology presents us with new and compelling opportunities for discovery when focused on the world's natural history collections. The outstanding barrier to applying existing and forthcoming computational methods for... more
Digital technology presents us with new and compelling opportunities for discovery when focused on the world's natural history collections. The outstanding barrier to applying existing and forthcoming computational methods for large-scale study of this important resource is that it is (largely) not yet in the digital realm. Without development of new and much faster methods for digitizing objects in these collections, it will be a long time before these data are available in digital form. For example, methods that are currently employed for capturing, cataloguing, and indexing pinned insect specimen data will require many tens of years or more to process collections with millions of dry specimens, and so we need to develop a much faster pipeline. In this paper we describe a capture system capable of collecting and archiving the imagery necessary to digitize a collection of circa 4.5 million specimens in one or two years of production operation. To minimize the time required to d...
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The South Pole Infrared Explorer is the name given a series of experiments to determine the suitability of the South Pole as a site for near infrared astrophysics observations. For the first phase of this project we have constructed a 60... more
The South Pole Infrared Explorer is the name given a series of experiments to determine the suitability of the South Pole as a site for near infrared astrophysics observations. For the first phase of this project we have constructed a 60 cm telescope and a near infrared imaging spectrometer. With this instrumentation we plan to carry out a program of measurements to test the qualities of the site. We also plan to carry out a survey for faint galaxies. Between December of 1993 and February of 1994 we began to place the equipment at the Pole. ...
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This paper presents an analytical model for parallel volume rendering of large datasets using GPU-based clusters. The model is focused on the parallel volume rendering and compositing stages and predicts their performance requiring only a... more
This paper presents an analytical model for parallel volume rendering of large datasets using GPU-based clusters. The model is focused on the parallel volume rendering and compositing stages and predicts their performance requiring only a few input parameters. We also present vl3, a novel parallel volume rendering framework for visualization of large datasets. Its performance is evaluated on a GPU-based cluster, weak and strong scaling are studied, and model predictions are validated with experimental results on up to 128 GPUs.
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Some basic ideas and recent developments in gravitational radiation detectors using laser interferometry are described, with emphasis on optical cavity interferometers and on methods of improving detector sensitivity for particular kinds... more
Some basic ideas and recent developments in gravitational radiation detectors using laser interferometry are described, with emphasis on optical cavity interferometers and on methods of improving detector sensitivity for particular kinds of signal.
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ABSTRACT The light from early galaxies had a dramatic impact on the gasses filling the universe. This video highlights the spatial structure of the light's effect, by comparing two simulations: one with a self-consistent radiation... more
ABSTRACT The light from early galaxies had a dramatic impact on the gasses filling the universe. This video highlights the spatial structure of the light's effect, by comparing two simulations: one with a self-consistent radiation field (radiative), and one without (non-radiative), each with a very high dynamic range. Looking at the simulations side-by-side it's hard to see any difference. However, because the simulations have the same initial conditions, we can directly compare them, by looking at the relative difference of the density. The coral-like blobs are regions where light has radiated out, heating the gas, and raising the pressure. The red regions show where the density is much higher in the radiative simulation, while the yellow regions are where the non-radiative has more density, showing where gravity was able to pull the filaments into tighter cylinders, without having to work against pressure from stellar heating. This is the first known visualization of this process, known as Jeans smoothing.