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Papers

Zeno Software

ZENO: Software for calculating hydrodynamic, electrical, and shape properties of polymer and particle suspensions
Derek Juba, Debra J. Audus, Michael Mascagni, Jack F. Douglas, and Walid Keyrouz
Journal of Research of the National Institute of Standards and Technology
Volume 122, Year 2017

Zeno

Acceleration and Parallelization of ZENO/Walk-on-Spheres
Derek Juba, Walid Keyrouz, Michael Mascagni, and Mary Brady
Procedia Computer Science
Volume 80, Pages 269-278, Year 2016

Survey

Survey statistics of automated segmentations applied to optical imaging of mammalian cells
Peter Bajcsy, Antonio Cardone, Joe Chalfoun, Michael Halter, Derek Juba, Marcin Kociolek, Michael Majurski, Adele Peskin, Carl Simon, Mylene Simon, Antoine Vandecreme, and Mary Brady
BMC Bioinformatics
Volume 16, Page 330, Year 2015

Segmentation

A method for the evaluation of thousands of automated 3D stem cell segmentations
Peter Bajcsy, Mylene Simon, Stephen J. Florczyk, Carl G. Simon Jr., Derek Juba, and Mary C. Brady
Journal of Microscopy
Volume 260, Issue 3, Pages 363-376, Year 2015

Cylinder

Parallel Geometric Classification of Stem Cells by Their 3D Morphology
Derek Juba, Antonio Cardone, Cheuk Yiu Ip, Carl G. Simon Jr., Christopher K. Tison, Girish Kumar, Mary Brady, and Amitabh Varshney
Computational Science and Discovery
Volume 6, Number 1, 015007, Year 2013

Turbulence

Using graphics processors for high-performance computation and visualization of plasma turbulence
George Stantchev, Derek Juba, William Dorland, and Amitabh Varshney
Computing in Science and Engineering
Volume 11, Number 2, Pages 52-59, Year 2009

Torus

Confluent Volumetric Visualization of Gyrokinetic Turbulence
George Stantchev, Derek Juba, William Dorland, and Amitabh Varshney
IEEE Transactions on Plasma Science
Volume 36, Number 4, Pages 1112-1113, Year 2008

Molecule

Parallel, Stochastic Measurement of Molecular Surface Area
Derek Juba and Amitabh Varshney
Journal of Molecular Graphics and Modelling
Volume 27, Number 1, Pages 82-87, Year 2008
Source Code

Posters

Zeno demo

ZENO: an efficient code for computing particle properties
Derek Juba, Debra J. Audus, Jack F. Douglas, Michael V. A. Mascagni, and Walid Keyrouz
CHiMaD 2016

Scaffolds

Effect of Biomaterial Scaffolds on 3D Shape of Stem Cells
Stephen J. Florczyk, Mylene Simon, Derek Juba, Sumona Sarkar, Desu Chen, Paula J. Baker, Antonio Cardone, Peter Bajcsy, Mary Brady, and Carl G. Simon, Jr.
TERMIS-AM 2014

Scaffolds

Effect of Scaffold Structure on 3D Shape of Stem Cells
Derek Juba, Antonio Cardone, Desu Chen, Stephen J. Florczyk, Sumona Sarkar, Carl G. Simon, Jr., and Mary Brady
Annual Meeting of the Society For Biomaterials 2014

Tech Reports

Torso

Modelling and Rendering Large Volume Data with Gaussian Radial Basis Functions
Derek Juba and Amitabh Varshney
Tech. Rep. UMIACS-TR-2007-22, University of Maryland, College Park