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Displaying 26 - 50 of 111

From Image Tiles to Web-Based Interactive Measurements in One Stop

January 4, 2017
Author(s)
Antoine Vandecreme, Michael P. Majurski, Joe Chalfoun, Keana Scott, John Henry Scott, Mary C. Brady, Peter Bajcsy
This article aims at introducing readers to a web-based solution useful for interactive measurements of centimeter-sized specimens at nanoscales. Modern imaging technology has enabled nanoscale imaging to become a routine process. As the imaging technology

An Informatics Infrastructure for the Materials Genome Initiative

July 6, 2016
Author(s)
Alden A. Dima, Sunil K. Bhaskarla, Chandler A. Becker, Mary C. Brady, Carelyn E. Campbell, Philippe J. Dessauw, Robert J. Hanisch, Ursula R. Kattner, Kenneth G. Kroenlein, Adele P. Peskin, Raymond L. Plante, Guillaume Sousa Amaral, Zachary T. Trautt, James A. Warren, Sharief S. Youssef, Sheng Yen Li, Pierre Francois Rigodiat, Marcus W. Newrock
A materials data infrastructure that enables the sharing and transformation of a wide range of materials data is an essential part of achieving the goals of the Materials Genome Initiative. We describe two high-level requirements of such an infrastructure

Enabling Interactive Measurements from Large Coverage Microscopy

July 1, 2016
Author(s)
Peter Bajcsy, Antoine Vandecreme, Julien M. Amelot, Mary C. Brady, Joe Chalfoun, Michael P. Majurski
Microscopy could be an important tool for characterizing stem cell products if quantitative measurements could be collected over multiple spatial and temporal scales. With the cells changing states over time and being several orders of magnitude smaller

Methodology for Increasing Image Feature Measurement Accuracy

June 30, 2016
Author(s)
Michael Paul Majurski, Joe Chalfoun, Steven Lund, Peter Bajcsy, Mary C. Brady
Motivation Image features are computed in cell biology to derive quantitative information regarding cell state, differentiation, biological activity, and cell dynamics. The accuracy of any biological conclusions depends on the accuracy of the measured

Acceleration and Parallelization of ZENO/Walk-on-Spheres

June 1, 2016
Author(s)
Derek Juba, Walid Keyrouz, Michael V. Mascagni, Mary C. Brady, Michael Mascagni
This paper describes our on-going work to accelerate ZENO, a software tool based on Monte Carlo methods (MCMs), used for computing material properties at the nanoscale. ZENO employs three main algorithms: (1)Walk on Spheres (WoS), (2)interior sampling, and

3D Segmentation of Stem Cells from Thousands of Confocal Microscopy Images

March 1, 2016
Author(s)
Peter Bajcsy, Mylene H. Simon, Stephen J. Florczyk, Carl G. Simon Jr., Derek Juba, Mary C. Brady
We address the problem of estimating 3D segmentation performance when segmentation is applied to thousands of confocal microscopy images (z-stacks) of cells. With a very large number of z-stacks, manual inputs to validate each segmentation result are

Survey Statistics of Automated Segmentations Applied to Optical Imaging of Mammalian Cells

January 8, 2016
Author(s)
Peter Bajcsy, Antonio Cardone, Joe Chalfoun, Michael W. Halter, Derek Juba, Marcin Kociolek, Michael P. Majurski, Adele P. Peskin, Carl G. Simon Jr., Mylene H. Simon, Antoine Vandecreme, Anne L. Plant, Mary C. Brady
The goal of this survey paper is to overview cellular measurements using optical microscopy imaging followed by automated image segmentation. The cellular measurements of primary interest are taken from mammalian cells and their components. They are

A Hybrid Task Graph Scheduler for High Performance Image Processing Workflows

December 16, 2015
Author(s)
Timothy J. Blattner, Walid Keyrouz, Milton Halem, Shuvra S. Bhattacharyya, Mary C. Brady
The scalability of applications is a key requirement to improving performance in hybrid and cluster computing. Scheduling code to utilize parallelism is difficult, particularly when dealing with dependencies, memory management, data motion, and processor

Shape Descriptors Comparison for Cell Tracking

October 15, 2015
Author(s)
Michael P. Majurski, Christopher Zheng, Joe Chalfoun, Alden A. Dima, Mary C. Brady
New microscope technologies are enabling the acquisition of large volumes of live cell image data. Accurate temporal object tracking is required to facilitate the analysis of this data. One principle component of cell tracking is correspondence, matching