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Search Publications by: Peter Bajcsy ()

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Displaying 26 - 50 of 58

Modeling, Validation and Verification of Three-Dimensional Cell-Scaffold Contacts from Terabyte- sized Images

December 1, 2017
Author(s)
Peter Bajcsy, Sowon Joy Yoon, Stephen Florczyk, Nathan Hotaling, Mylene H. Simon, Piotr Szczypinski, Nicholas J. Schaub, Carl G. Simon Jr., Mary C. Brady, Ram D. Sriram
Background: Cell-scaffold contact measurements are derived from pairs of co-registered volumetric fluorescent confocal laser scanning microscopy (CLSM) images (z-stacks) of stained cells and spun coat, large microfiber, and medium microfiber scaffolds. Our

3D Cellular Morphotyping of Cell Niches

August 31, 2017
Author(s)
Stephen J. Florczyk, Mylene H. Simon, Derek Juba, Patrick S. Pine, Sumona Sarkar, Desu Chen, Paula J. Baker, Subhadip Bodhak, Antonio Cardone, Mary C. Brady, Peter Bajcsy, Carl G. Simon Jr.
Three-dimensional (3D) cellular morphotyping is introduced for assessing and comparing the niches provided by biomaterial scaffolds. Many scaffold systems have been advanced to provide synthetic cell niches for tissue engineering and drug screening

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

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

Large-scale Time-lapse Microscopy of Oct4 Expression in Human Embryonic Stem Cell Colonies

May 22, 2016
Author(s)
Kiran Bhadriraju, Michael Halter, Julien M. Amelot, Peter Bajcsy, Joe Chalfoun, Antoine Vandecreme, Barbara Mallon, Kye-yoon Park, John T. Elliott, Subhash Sista, Anne L. Plant
Identification of critical characteristics of therapeutically active cells, and quantification of those characteristics, are essential for assuring consistency and potency of cell therapy products. We have developed image analysis and visualization

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

Confidence Estimation in Stem Cell Classification

October 15, 2015
Author(s)
Peter Bajcsy, Jana Kosecka, Zahra Rajabi
We study the problem of supervised classification of stem cell colonies and confidence estimation of the attained classification labels. The problem is investigated in the application context of heterogeneity labels of stem cell colonies observed by using

Quantifying CD4 receptor protein in two human CD4+ lymphocyte preparations for quantitative flow cytometry

December 11, 2014
Author(s)
Meiyao M. Wang, Martin Misakian, Hua-Jun He, Peter Bajcsy, Jeffrey M. Davis, Kenneth D. Cole, Illarion Turko, Lili Wang, Fatima Abbasi
For quantitative flow cytometry, a biological cell reference material with a known biomarker expression level is needed to transform a linear arbitrary fluorescence intensity scale obtained with fluorescent microspheres to an antibody bound per cell (ABC)

Spatial Computations over Terabyte-Sized Images on Hadoop Platforms

October 27, 2014
Author(s)
Peter Bajcsy, Antoine Vandecreme, Mary C. Brady, Phuong Nguyen
Our objective is to lower the barrier of executing spatial image computations in a computer cluster/cloud environment instead of in a desktop/laptop computing environment. We research two related problems encountered during an execution of spatial

Automated Ranking of Stem Cell Colonies by Translating Biological Rules to Computational Models

September 20, 2014
Author(s)
Adele P. Peskin, Steven P. Lund, YaShian Li-Baboud, Michael W. Halter, Anne L. Plant, Peter Bajcsy
This paper addresses the problem of automating an image ranking process for stem cell colonies. We automate the manual process in a novel way: instead of fitting off-the-shelf image features and colony ranks to prediction models, we define a new feature

Measuring Organelle Shape in 3D in Stem Cells Cultured on Nanofiber Scaffolds

April 19, 2014
Author(s)
Carl G. Simon Jr., Peter Bajcsy, Wojtek J. Tutak, Jyotsnendu J. Giri
Previous work has demonstrated that culture of osteoprogenitor cells on nanofiber scaffolds can potentiate osteogenic differentiation [1-4]. Culture of cells in nanofiber scaffolds causes changes to cell morphology, suggesting that morphological changes

Calibrating multiple microscopes with a smartphone

April 1, 2014
Author(s)
Peter Bajcsy, Mary C. Brady, Jacob Siegel
Summary: The iPhone liquid crystal displays allows efficient and accurate calibration of an inexpensive array of handheld microscopes for measuring microscopic dynamic events over a large field of view. How does one build an inexpensive array of handheld

Re-Projection of Terabyte-sized 3D Images for Interactive Visualization

October 9, 2013
Author(s)
Peter Bajcsy, Antoine Vandecreme, Mary C. Brady
How does one inspect terabyte-sized 3D images visually from multiple viewpoints? The current solutions are limited to gigabyte-sized images using specialized hardware to achieve interactivity and lacking the ability to share data for collaborative research

Re-projection of Terabyte-Sized Images

October 7, 2013
Author(s)
Peter Bajcsy, Antoine Vandecreme, Mary C. Brady
This work addresses the problem of re-projecting a terabyte-sized 3D data set represented as a set of 2D Deep Zoom pyramids. In general, a re-projection for small 3D data sets is executed directly in RAM. However, RAM becomes a limiting factor for terabyte

Terabyte Size Image Computations on Hadoop Cluster Platforms

October 7, 2013
Author(s)
Peter Bajcsy, Antoine Vandecreme, Julien M. Amelot, Phuong T. Nguyen, Joe Chalfoun, Mary C. Brady
We present a characterization of four basic terabyte size image computations on a Hadoop cluster in terms of their relative efficiency according to the modified Amdahl’s law. The work is motivated by the fact that there is a lack of standard benchmarks and

Segmenting Time-lapse Phase Contrast Images of Adjacent NIH 3T3 Cells

January 15, 2013
Author(s)
Joe Chalfoun, Alden A. Dima, Marcin Kociolek, Michael W. Halter, Antonio Cardone, Adele P. Peskin, Peter Bajcsy, Mary C. Brady
We present a new method for segmenting phase contrast images of NIH 3T3 fibroblast cells that is accurate even when cells are in contact. The problem of segmentation, when cells are in contact, poses a challenge to the accurate automation of cell counting