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Eric Wait, Mark Winter, Chris Bjornsson, Erzsebet Kokovay, Yue Wang, Susan Goderie, Sally Temple, Andrew Cohen
RESULTS: We present an application that enables the quantitative analysis of multichannel 5-D (x, y, z, t, channel) and large montage confocal fluorescence microscopy images. The image sequences show stem cells together with blood vessels, enabling quantification of the dynamic behaviors of stem cells in relation to their vascular niche, with applications in developmental and […]
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Tobias Brix, Jorg-Stefan Prassni, Klaus Hinrichs
BACKGROUND: Visualization of multi-channel microscopy data plays a vital role in biological research. With the ever-increasing resolution of modern microscopes the data set size of the scanned specimen grows steadily. On commodity hardware this size easily exceeds the available main memory and the even more limited GPU memory. Common volume rendering techniques require the entire […]
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George Teodoro, Tony Pan, Tahsin Kurc, Jun Kong, Lee Cooper, Scott Klasky, Joel Saltz
Distributed memory machines equipped with CPUs and GPUs (hybrid computing nodes) are hard to program because of the multiple layers of memory and heterogeneous computing configurations. In this paper, we introduce a region template abstraction for the efficient management of common data types used in analysis of large datasets of high resolution images on clusters […]
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George Teodoro, Tahsin Kurc, Jun Kong, Lee Cooper, Joel Saltz
We investigate and characterize the performance of an important class of operations on GPUs and Many Integrated Core (MIC) architectures. Our work is motivated by applications that analyze low-dimensional spatial datasets captured by high resolution sensors, such as image datasets obtained from whole slide tissue specimens using microscopy image scanners. We identify the data access […]
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Thai V. Hoang, Xavier Cavin, Patrick Schultz, David W. Ritchie
BACKGROUND: Picking images of particles in cryo-electron micrographs is an important step in solving the 3D structures of large macromolecular assemblies. However, in order to achieve sub-nanometre resolution it is often necessary to capture and process many thousands or even several millions of 2D particle images. Thus, a computational bottleneck in reaching high resolution is […]
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Thai V. Hoang, Xavier Cavin, David W. Ritchie
Fitting high resolution protein structures into low resolution cryo-electron microscopy (cryo-EM) density maps is an important technique for modeling the atomic structures of very large macromolecular assemblies. This article presents "gEMfitter", a highly parallel fast Fourier transform (FFT) EM density fitting program which can exploit the special hardware properties of modern graphics processor units (GPUs) […]
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Sandor Szenasi, Zoltan Vamossy
The use of digital microscopy allows diagnosis through automated quantitative and qualitative analysis of the digital images. Often to evaluate the samples, the first step is determining the number and location of cell nuclei. For this purpose, we have developed a GPGPU based data-parallel region growing algorithm that is equally as accurate as the already […]
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Stephan Preibisch, Fernando Amat, Evangelia Stamataki, Mihail Sarov, Eugene Myers, Pavel Tomancak
Light sheet fluorescence microscopy is able to image large specimen with high resolution by imaging the samples from multiple angles. Multi-view deconvolution can significantly improve the resolution and contrast of the images, but its application has been limited due to the large size of the datasets. Here we present a derivation of multi-view Bayesian deconvolution […]
Andrej Krejcir
The aim of the thesis is to implement and optimize chosen image processing algorithms used in digital holographic microscopy on the GPU. The algorithms are 2-D phase unwrapping and polynomial surface fitting. They are described and certain used optimizations are pointed out. The results chapter shows the performance and precision of the GPU implementation compared […]
Fernando Amat, Philipp J. Keller
Object detection and classification are key tasks in computer vision that can facilitate high-throughput image analysis of microscopy data. We present a set of local image descriptors for three-dimensional (3D) microscopy datasets inspired by the well-known Haar wavelet framework. We add orientation, illumination and scale information by assuming that the neighborhood surrounding points of interests […]
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George Teodoro, Tony Pan, Tahsin M. Kurc, Jun Kong, Lee A. D. Cooper, Norbert Podhorszki, Scott Klasky, Joel H. Saltz
Analysis of large pathology image datasets offers significant opportunities for biomedical researchers to investigate the morphology of disease, but the resource requirements of image analyses limit the scale of those studies. Motivated by such a study, we propose and evaluate a parallel image analysis application pipeline for high throughput computation of large datasets of high […]
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Giovanni Cerchiari, Fabrizio Croccolo, Frederic Cardinaux, Frank Scheffold
We present an implementation of the analysis of dynamic near field scattering (NFS) data using a graphics processing unit (GPU). We introduce an optimized data management scheme thereby limiting the number of operations required. Overall, we reduce the processing time from hours to minutes, for typical experimental conditions. Previously the limiting step in such experiments, […]
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