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1. 3D Segmentation of Stem Cells from Thousands of Confocal Microscopy Images
Peter Bajcsy, Mylene Henriqueta Monique Simon, Stephen J Florczyk, Carl George 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 ...
2. Automated Ranking of Stem Cell Colonies by Translating Biological Rules to Computational Models
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 feat ...
3. Background Intensity Correction for Terabyte-Sized Time-Lapse Images
Joe Chalfoun, Michael P Majurski, Kiran Bhadriraju, Steven P Lund, Peter Bajcsy, Mary C Brady
4. Calibrating multiple microscopes with a smartphone
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 ha ...
5. Conformance of Image Features to Classifier Assumptions
Julien M. Amelot, Peter Bajcsy, Mary C Brady
Cell measurements are derived frequently from the results of pixel classification and contiguous
region segmentation of microscopy images. Image segmentation is accomplished by classifying image
pixels based on high dimensional image features com ...
6. Data Quality for High Content Screening
YaShian Li-Baboud, Oleg Aulov, Peter Bajcsy
TO HAVE CONFIDENCE IN THE KNOWLEDGE GLEANED FROM DATA, IT IS ESSENTIAL TO VERIFY THE QUALITY OF THE DATA
SOURCES AND TO HAVE A MEANS OF QUANTIFYING THE POTENTIAL UNCERTAINTIES DUE TO THE QUALITY OF DATA FOR MAKING
CRITICAL, INTELLIGENT DECISIONS. ...
7. Grand Challenges of Measurement Science with Big Data
This presentation discusses Grand Challenges of Measurement Science with Big Data. It illustrates the difference between Measurement Science with Little Data and Big Data in the domain of cell biology and microscopy image observations.
8. Measuring Organelle Shape in 3D in Stem Cells Cultured on Nanofiber Scaffolds
Carl George 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 ...
9. Quantifying CD4 receptor protein in two human CD4+ lymphocyte
preparations for quantitative flow cytometry
Meiyao M. Wang, Martin Misakian, Hua-Jun He, Peter Bajcsy, Jeffrey M. Davis, Kenneth D Cole, Illarion V 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 c ...
10. Re-projection of Terabyte-Sized Images
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 te ...