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1. Background Intensity Correction for Terabyte-Sized Time-Lapse Images
Published: 12/30/2014
Authors: Joe Chalfoun, Michael P Majurski, Kiran Bhadriraju, Steven P Lund, Peter Bajcsy, Mary C Brady

2. Quantifying CD4 receptor protein in two human CD4+ lymphocyte preparations for quantitative flow cytometry
Published: 12/11/2014
Authors: Meiyao M. Wang, Martin Misakian, Hua-Jun He, Peter Bajcsy, Jeffrey M. Davis, Kenneth D Cole, Illarion V Turko, Lili Wang, Fatima Abbasi
Abstract: 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 c ...

3. Automated Ranking of Stem Cell Colonies by Translating Biological Rules to Computational Models
Published: 9/20/2014
Authors: Adele P Peskin, Steven P Lund, YaShian Li-Baboud, Michael W Halter, Anne L Plant, Peter Bajcsy
Abstract: 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 feat ...

4. Measuring Organelle Shape in 3D in Stem Cells Cultured on Nanofiber Scaffolds
Published: 4/19/2014
Authors: Carl George Simon Jr., Peter Bajcsy, Wojtek J Tutak, Jyotsnendu J. Giri
Abstract: 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 ...

5. Calibrating multiple microscopes with a smartphone
Published: 4/1/2014
Authors: Peter Bajcsy, Mary C Brady, Jacob Siegel
Abstract: 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 ha ...

6. Re-projection of Terabyte-Sized Images
Published: 10/7/2013
Authors: Peter Bajcsy, Antoine Vandecreme, Mary C Brady
Abstract: 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 te ...

7. Terabyte Size Image Computations on Hadoop Cluster Platforms
Published: 10/7/2013
Authors: Peter Bajcsy, Antoine Vandecreme, Julien M. Amelot, Phuong Thi Thu Nguyen, Joe Chalfoun, Mary C Brady
Abstract: 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 benchmar ...

8. Understanding impact of image quality on segmentation accuracy
Published: 8/6/2013
Authors: YaShian Li-Baboud, Antonio Cardone, Joe Chalfoun, Peter Bajcsy, John T Elliott
Abstract: We introduce a methodology for microscopy settings assessment and segmentation accuracy prediction based on image quality descriptors.

9. Segmenting Time-lapse Phase Contrast Images of Adjacent NIH 3T3 Cells
Published: 1/15/2013
Authors: Joe Chalfoun, Alden A Dima, Marcin Kociolek, Michael W Halter, Antonio Cardone, Adele P Peskin, Peter Bajcsy, Mary C Brady
Abstract: 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 cou ...

10. Versus: A Framework for General Content-Based Comparisons
Published: 10/8/2012
Authors: Peter Bajcsy, Antoine Vandecreme, Benjamin J Long, Paul Khouri Saba, Joe Chalfoun, Luigi Marini, Rob Kooper, Michal Ondrejcek, Kenton McHenry, Smruti Padhy
Abstract: Versus is a framework for the execution and dissemination of customizable content-based file comparison methods. Given digital objects such as files, database entries, or in-memory data structures, we are interested in establishing their proximity (i ...

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