Associate Professor Biomedical Engineering Phone: 412 268 3684

Associate Professor Biomedical Engineering Phone: 412 268 3684
Gustavo Kunde Rohde, Ph.D.
Associate Professor
Biomedical Engineering
Electrical and Computer Engineering
Computational Biology
C 120, Hamerschlag Hall
Carnegie Mellon University
5000 Forbes Avenue
Pittsburgh, PA, 15213
Phone: 412 268 3684
Fax: 412 268 9580
[email protected]
http://www.andrew.cmu.edu/~gustavor
Date: Jan 4, 2016.
Education
Ph.D. Applied Mathematics and Scientific Computation, University of Maryland, 2005. Thesis
advisors: Dennis M. Healy, Jr., and Carlos A. Berenstein.
M.S. Electrical Engineering, Vanderbilt University, 2001. Thesis advisors: Benoit M. Dawant,
and Akram Aldroubi.
B.S. Physics and Mathematics, Vanderbilt University, 1999
Appointments
BME, ECE, Computational Biology Departments
Associate Professor
Carnegie Mellon University
2012 – present
BME, ECE, Computational Biology Departments
Assistant Professor
Carnegie Mellon University
2007 – 2012
National Research Council, National Academies
Postdoctoral Research Associate
Naval Research Laboratory
2005–2006
Section on Tissue Biophysics and Biomimetics
Research Assistant
National Institutes of Health
2001-2005
Systems Planning Corporation
Consultant
Washington DC, USA
2005
Medical Image Processing Laboratory, EECE
Research Assistant
Vanderbilt University
1999–2001
Brief biography
Dr. Rohde was born in 1977 in Porto Alegre, state of Rio Grande do Sul, Brazil. He immigrated
to the United States of America in 1992 where he attended a portion of high school, college, and
graduate school. He is a citizen of the United States of America.
Gustavo Kunde Rohde
Affiliations
Center for Bioimage Informatics
Carnegie Mellon University
2007-present
Center for the Neural Basis of Cognition
Carnegie Mellon University
2013-present
Current Research Support
National Science Foundation (CCF 1421502): 9/1/2014 – 8/31/2017. PI: Rohde. Title: CIF:
Small: Transport and other Lagrangian transforms for signal analysis and discrimination. U$
499,999. Rohde effort: 0.85 months/year.
National Institutes of Health R01 (DK103002): 7/01/14-6/30/2018. PI: Husain (Rohde PI of
CMU subcontract). Title: HDACs in pancreatic recovery after injury. U$ 100,000. Rohde
effort: 0.5 months/year.
National Institutes of Health R21: 2014-2016. PI: Rohde. Title: Utility of Effusion Cytology
and Image Analysis in the Diagnosis of Mesothelioma. Direct costs: U$ 190,000. Rohde effort:
1.5 months/year.
National Institutes of Health P41: 2012-2017 (GM103712). PI: Bahar. Title: HighPerformance Computing for Multiscale Modeling of Biological Systems. Role: Co-PI. Direct
costs: U$ 7,756,810 ($1,551,347 sub award to CMU). Rohde effort: 1 month/year.
National Institutes of Health R01: 2015-2020 (GM090033). PI: Rohde, Murphy. Title: Imagederived Spatiotemporal Models of Cellular Organization and Perturbation. Direct costs: U$
1,100,000. Rohde effort: 1 month/year.
CMU-Portugal Entrepreneurial Research Initiatives (CMUP-ERI/TIC/0028), 4/1/20163/31/2020, CMU PI: Rohde. Title: Screen-DR – Image Analysis and Machine Learning
Platform for Innovation in Diabetic Retinopathy Screening, U$690,055. Rohde effort: 1
month/year.
Past Research Support
National Institutes of Health R01: 2010-2015 (GM090033). PI: Rohde. Title: Automated HighThroughput Estimation and Modeling of Protein Network Distributions. Direct costs: U$
800,000. Rohde effort: 2 months/year.
Naval Research Laboratory research grant: 2014-2015. PI: Rohde. Title: A system for spectral
signal classification. Direct costs: U$ 22,500. Rohde effort: 0.85 months/year.
Pennsylvania State Health Department (4100059192), CURE program: 2012-2014. PI:
Murphy. Title: Automated Biomarker Identification for Cancer Detection and Prognosis. Role:
Co-PI. Direct costs: U$ 842,063. Rohde effort: 1 month/year.
Gustavo Kunde Rohde
National Institutes of Health R21: 2009-2012 (GM088816) PI: Rohde. Title: Deformationbased computational morphometry for cell biology applications. Role: PI. Direct costs: U$
225,000. Rohde effort: 1 month/year.
Pennsylvania Infrastructure Technology Alliance (PITA), Commonwealth of Pennsylvania’s
Department of Community and Economic Development, 2009-2010. PI: Rohde. Title: Towards
non-invasive radi¬ological diagnosis by automated learning from MRI and histology image
data. Role: PI. , Direct costs: U$65,000. Rohde effort: 0.5 months/year.
Pennsylvania Department of Health through the Tobacco Settlement Fund: 2009. PI: Rohde.
Title: High-Throughput Estimation and Modeling of Protein Filament Distributions from
Microscope Images. Direct costs: U$ 35,000. Rohde effort: 0.5 months/year.
Awards
National Research Council, National Academies, post doctoral fellowship. Title: Fundamental
Limits of Information-theoretic Approaches in Probabilistic Signal Detection. Period: 20052006.
Entrepreneurial Activities
Founder (2015) and Co-owner, Smoke Detective LLC.
Society Memberships
Institute of Electrical and Electronics Engineers (IEEE)
International Society for Advancement of Cytometry (ISAC)
International Society for Advancement of Cytometry (ISAC) Council Member
Editorial Roles
IEEE Transactions on Image Processing, Associate Editor, 2016 – present.
IEEE Signal Processing Letters, Associate Editor, 2012-2014.
BMC Bioinformatics, Associate Editor, 2012-present.
IEEE Journal of Biomedical and Health Informatics, Associate Editor, 2014-present.
Editorial Board Member, Cytometry A, 2014 – present.
Gustavo Kunde Rohde
Service
International Society for Analytical Cytology (ISAC) Educational Committee, Image
Cytometry Content Task Force leader, 2012-present.
International Society for Analytical Cytology (ISAC) Educational Committee Member 2007present.
IEEE Biomedical Imaging and Signal Processing Technical Committee. Member, 2011present.
IEEE Biomedical Imaging and Signal Processing Technical Committee. Associate member,
2007-2010.
Major Conference Roles
Organizing Committee, CYTO 2016 congress (Seattle, USA), International Society for
Advancement of Cytometry.
Organizing Committee, CYTO 2015 congress (Glasgow, Scotland), International Society for
Advancement of Cytometry.
Organizing Committee, ISBI 2015 (New York, New York, USA), IEEE.
Organizing Committee, CYTO 2014 congress (Orlando, Florida, USA), International Society
for Advancement of Cytometry.
Area chair: IEEE International Conference on Image Processing (ICIP), 2013.
Special session organizer: IEEE EMBC 2013. Image-based cytometry, technology and
applications, Osaka, Japan.
CYTO (International Society for Advancement of Cytometry) 2013, pre-congress course on
image cytometry. Role: organizer.
Workshop Organizer. Title: Computational Methods for Learning from Cell Images. Workshop
at CYTO 2012 congress.
Session chair: Asilomar 2007, IEEE ISBI 2008, IEEE ISBI 2009, IEEE ISBI 2011, IEEE ISBI
2012, CYTO 2008, CYTO 2010, CYTO 2012, IEEE EMBC 2013, CYTO 2013, CYTO 2014.
Local Organizing Committee, Bioimage Informatics meeting, Carnegie Mellon University,
Pittsburgh, PA, 2010.
CYTO (International Society for Advancement of Cytometry) 2010, pre-congress course on
image cytometry. Role: organizer.
Gustavo Kunde Rohde
Tutorial on Image Registration, International Symposium on Biomedical Imaging (ISBI) 2010
Special session organizer. Title: Image Registration in Bioimaging. Asilomar conference on
Signals, Systems and Computers, 2007.
Reviewing
NIH ZRG1 IMST-S 42 B, program project reviewer, April, 2014.
Frederick National Laboratory Visiting Scholar Program grant reviewer, 2013.
National Institutes of Health, Biodata Management and Analysis study section, panel
discussion member, February 2013.
NIH RC1 Grand Opportunities grant review panel. Special emphasis review group 2009/10
ZRG1 GGG-A (99) S, August 13th, 2009.
Ad hoc reviewer: National Science Foundation, National Institutes of Health, USA.
Ad hoc reviewer: Biomedical Engineering OnLine, International Journal of Adaptive Control
and Signal Processing, IEEE Transactions on Medical Imaging, IEEE Transactions on Image
Processing, IEEE Trans. on Signal Processing, Journal of Mathematical Imaging and Vision,
Neuroimage, Computers in Biology and Medicine, Cytometry A, IEEE Signal Processing
Magazine, Elsevier Signal Processing, Physica D, Medical Physics, Pattern Recognition
Letters, Molecular Biology of the Cell, Journal of Microscopy, SIAM Journal on Imaging
Sciences, Optics Express, Journal of Pathology Informatics, Nature Biotechnology, PLOS
Computational Biology, PLOS One, Image and Vision Computing, Bioinformatics, BMC
Bioinformatics, and several other journals.
Program Technical Committee: Brazilian Symposium on Computer Graphics and Image
Pro¬cessing (2007 and 2008). ICASSP 08,09,11,12, 13,14,15. ICIP 12,13,14. ISBI
08,09,11,12, 13,14,15. MICCAI 09. International Symposium on Visual Computing
(Computational Bioimaging track) 09, IEEE Int. Conf. On Bioinformatics & Biomedicine 09.
ISMB 2011, 2012, CYTO 13, 14, 15, GLBIO 2013. ICIAR 2013.
Invited Research Talks and Tutorials
“Processing methods for enhancement, physiological measurement, and automated learning
from optical signals,” Advances in Optics for Biotechnology, Medicine, and Surgery XIV,
Vail, Colorado. Invited presentation, June 16, 2015.
“PCA-based super resolution in transport space,” Computational Optical Sensing and Imaging
(COSI), Imaging and Applied Optics Congress, Arlington, Virginia, USA. Invited presentation,
June 11, 2015
Gustavo Kunde Rohde
“Signal processing and biomarker discovery,” South Australian Health & Medical Research
Institute, Adelaide, Australia, invited seminar, March 20, 2015.
“Understanding images of cells: limits and possibilities,” Outstanding Scientists Present
Seimnars, University of South Alabama College of Medicine, Mobile, Alabama, USA, March
12, 2015.
“Numerical methods for modeling and quantifying shape information of biological forms,”
National Center for Multiscale Modeling of Biological Systems, Carnegie Mellon University,
January 29, 2015.
“The optimal transport transform and its application to pattern recognition in image databases,”
Invited presentation, 5th International Conference on Computational Harmonic Analysis
(ICCHA 2014), Vanderbilt University, Nashville, TN, May 21st, 2014.
“Modeling information from images of cells.” Invited plenary talk (Frontiers Session), XXIX
Congress of the International Society for Advancement of Cytometry (CYTO 2014), Ft.
Lauderdale, Florida, USA. May 19th, 2014.
“Transport-based morphometry for modeling and discrimination of image data.” Workshop on
Morphogenesis, Regeneration, & the Analysis of Shape. February 11, 2014. Mathematical
Biosciences Institute, Ohio State University, Ohio, USA.
“How can image and data analysis help pathology research?” Pathology Department Seminar,
University of Pittsburgh, Pittsburgh, PA, 10/16/2013.
“New methods for quantifying and visualizing information from images of cells: an overview,”
Special Session on Image-based Cytometry: technology and applications. IEEE EMBC, Osaka,
Japan, July 2013.
“The linear optimal transport transform: why do we need it and how do we use it,” Big data &
Bioinformatics Seminar, Department of ECE, Virginia Tech. June 20, 2013.
“Telling one from another: modern methods for decoding cell morphology from microscopy
images with applications to pathology and cytology,” Laboratory of Pathology, National
Cancer Institute, NIH, June 19th, 2013.
“Telling one from another: modern methods for quantifying cell morphology,” Wirtz laboratory
seminar. Johns Hopkins University, June 18, 2013.
“Introduction to Image Processing and Analysis for Cytometry,” Pre CYTO 2013 congress
image cytometry course lecture, 18 May, 2013.
“A linear transport-based embedding method for analyzing biomedical images,” Biological
Image Analysis special session, Forty-Sixth Asilomar Conference on Signals, Systems and
Computers, Monterey, California. November 6, 2012.
Gustavo Kunde Rohde
“Tools for quantitative analysis of cellular morphology from histopathology images.” Division
of Biomedical Informatics monthly colloquium, University of Pittsburgh, October 12, 2012.
“New metrics for analyzing microscopy image data.” Computational Methods for Learning
from Cell Images. Workshop at CYTO 2012 congress, June 24th, 2012. Leipzig, Germany.
“Introduction to image analysis,” Lecture in CYTO 2012 pre-congress image cytometry course.
June 22nd, 2012. Leipzig, Germany.
“Image-based morphometry in medicine and biology: segmentation and visualization of
summarizing trends and discriminant information.” Biological Network Modeling Center
seminar, California Institute of Technology, Pasadena, California, May 16th, 2011.
“Image-based morphometry: segmentation and visualization of summarizing trends and
discriminant information.” MICe group seminar, Mouse Imaging Center, Hospital for Sick
Children, Toronto, CA, May 5th, 2011.
“Image-based morphometry: segmentation and visualization of summarizing trends and
discriminant information.” Biomedical Engineering Department Seminar, Carnegie Mellon
University, March 28th, 2011.
“Digital Image Processing” Lecture in CYTO 2010 Pre-congress image cytometry course. May
6th, 2010. Seattle, Washington.
“Detecting and classifying cancers from image data using optimal transportation,“ Biomedical
Image Analysis special session, 26th Southern Biomedical Engineering Conference, May 1st,
2010.
“Biomedical Image Registration: Overview of Principles” Tutorial at the International
Symposium on Biomedical Imaging, ISBI, 2010. April 14th, 2010. Rotterdam, The
Netherlands.
3rd,4th,5th,6th,7th (07,08,09,10,11) Annual Bioimaging Day. Center for Bioimage Informatics,
Carnegie Mellon University, Pittsburgh, PA, USA.
“Introduction to Image Analysis,” International Society for Advancement of Cytometry (ISAC)
pre congress course, Budapest, Hungary, May 16th 2008.
“Approximation and interpolation methods for biomedical image registration,” 41st Asilomar
conference on signals, systems and computers, November 2007. Pacific Grove, CA.
“Chaotic signal detection and estimation based on attractor sets: applications to secure
communications.” SIAM Conference on Applications of Dynamical Systems, May 2007. Utah,
USA.
Gustavo Kunde Rohde
“Stochastic analysis of geometric image processing using B-splines.” IEEE ICASSP, May
2006, Toulouse, France.
“Interpolation artifacts in sup-pixel image processing problems”, Center for Automation
Research Seminar, University of Maryland, May 12th, 2006. College Park, MD, USA.
“Sub-pixel variational image processing,” Analysis and Biomathematics Seminar, Department
of Mathematics, Vanderbilt University, February 21st, 2006. Nashville, TN, USA.
“Registration methods for quantitative biomedical imaging, ” CCB Presents Seminar Series,
Center for Computational Biology, UCLA, May 12th, 2005. Los Angeles, CA, USA.
“Registration methods for quantitative imaging,” Biomedical Engineering Seminar, Biomedical
Engineering Department, Vanderbilt University, February 3rd, 2005. Nashville, TN, USA.
“Image registration for correcting motion and distortion in di usion weighted magnetic
resonance imaging“, Harmonic Analysis Seminar, Department of Mathematics, University of
Maryland, September 23rd, 2004. College Park, MD, USA
Service at Carnegie Mellon University
Post-doctoral advisees:
Saurav Basu (2011- 2013)
Akif Burak Tosun (2012-2015)
Suchang Xu (2012-2013), visiting scholar
Fei Shang (2013-2014), visiting scholar
Ge Liang (2013-2014), visiting scholar
Miao Ma (2014-2015), visiting scholar
Soheil Kolouri (2015-present)
Yue Huang (2015-present), visiting scholar
Ph.D. students advised:
• Wei Wang (BME, 2007-2012), Liang Ji-Dian fellowship 2009. BME research award,
2011.
• Aabid Shari (CompBio, 2007-2012), Co-advised with Prof. R.F. Murphy
• Cheng (Andy) Chen (BME, 2008-2013), Liang Ji-Dian fellowship 2011.
• Soheil Kolouri (BME, 2012-2015), Bertucci Fellowship 2014, BME research award
2015.
• Se Rim Park (ECE, 2012-present)
• Shinjini Kundu (BME, 2013-present), ICES/Dowd Fellowship 2014/15.
• Chi Liu (BME, 2013-present)
• Yang Zou (BME, 2015-present)
Gustavo Kunde Rohde
M.S. students advised (thesis option only):
• Hu Huang (BME, 2011-2013)
• Jia Guo (BME, 2011-2013)
• Kan Jia (BME, 2013-2015)
• Ligong Han (BME, 2015-present)
Ph.D. thesis committees:
Charles Jackson (CMU BME, 2007-2009), Amina Chebira (CMU BME, 2007-2008),
Justin Newberg (CMU BME, 2007-2009), Tao Peng (CMU BME, 2008-2011), Judy
Schum (CMU BME, 2009¬2011), Suvrajit Maji (CMU BME, 2009-2012), Ramu
Bhagavatula (CMU ECE, 2010-2011), Daniel Delubac (CMU BME, 2010-2012),
Jieyue Li (CMU BME, 2012), Joshua Kangas (CMU CompBio, 2012-2013), Taraz
Buck (CMU CompBio, 2012-2013), Prahlad Menon (BME, 2012-2013), Nathan Lowry
(MIT, 2013), Aparna Kumar (CMU CompBio, 2013-2015), Devin Sullivan (CMU
CompBio,2013-2015), Gregory Johnson (CMU CompBio, 2014-present), Tim Jackson
(BME Pitt, 2015-present)
BME Department Biomedical Imaging and Signal Processing track advisor (~30 students)
BME Department Seminar Series Chair, 2013-2014.
CMU-Pitt Joint Computational Biology Graduate Program admissions committee, 2013present.
Undergraduate A airs Committee, Biomedical Engineering Department, 2007-present.
Joint CMU-University of Pittsburgh Computational Biology Program Curriculum Committee
2008¬present.
Joint CMU-University of Pittsburgh Computational Biology Program Admissions Committee
2008¬2009.
Bioimaging day, Carnegie Mellon University, 2008 organizer.
Center for Bioimage Informatics monthly lunchtime presentation series organizer (2007-2010).
Joint CMU/Pitt Computational Biology retreat co-organizer, August, 2008.
Teaching at Carnegie Mellon University
42-531 Computational Methods in Biomedical Engineering (Spring 2012-2015)
42-101 Introduction to Biomedical Engineering (Spring 2010, 2011)
42-431 (18496) Introduction to Biomedical Imaging and Image Analysis (Fall 2008-2015)
Gustavo Kunde Rohde
42-709: Readings in Bioimage Informatics (Spring 2008, 2009)
42-708: Special Topics: Registration in Bioimaging (Fall, 2007)
Patents
GK Rohde, F. Bucholtz, J. M. Nichols, Method and apparatus for secure digital
communications using chaotic signals, U.S. Patent #8385547. Issued on Feb 26, 2013.
W Wang, D Slepcev, GK Rohde, Quantitative comparison of image data using linear optimal
transportation, U.S. Patent Application serial no.:12/057275.
C. Chen, J. A. Ozolek, GK Rohde, Segmenting biological structures from microscopy images,
U.S. Patent Application serial no. 12/057504.
R. Mills, F. Lanni, S. Davis, GK Rohde, Fire Detection Apparatus Utilizing a Camera, U.S.
Patent Application N. 14,625,689
Publications
h-index: 22, citations: 2544
Google scholar: https://scholar.google.com/citations?user=UnRdQPMAAAAJ&hl=en
Book
1. GK Rohde, S. Kolouri, S. Basu, Introduction to Biomedical Imaging and Image
Analysis, in preparation. Accepted for publication by Cambridge University Press
(Cambridge Series in Biomedical Engineering), Expected publication date: Summer,
2016.
Peer Reviewed Book Chapters
1. S. Lockett and GK Rohde, Fluorescence Microscopy in Pathology, in Digital
Pathology, A. Parwani, L. Pantanowitz, Accepted for publication, 2015.
2. J. Kovacevic and GK Rohde, Overview of Image Analysis Tools and Tasks for
Microscopy, in Microscopic Image Analysis for Life Science Applications, J. Rittscher,
R. Machiraju and S. T. C. Wong, Eds., Artech House, 2008.
Preprints
1. S Kolouri, Y Zou, GK Rohde, Sliced Wasserstein Kernels for Probability Distributions,
arXiv:1511.03198, 2015.
2. SR Park, S Kolouri, S Kundu, GK Rohde, The Cumulative Distribution Transform and
Linear Pattern Classification, arXiv preprint arXiv:1507.05936, 2015.
Gustavo Kunde Rohde
3. S Kundu, S. Kolouri, GK Rohde, Multiscale Variational Optimal Transport for Medical
Imaging Applications, preprint, 2015.
Peer-reviewed Publications Appearing in Archived Journals
1. S Kolouri, SR Park, GK Rohde, The Radon cumulative distribution transform and its
application to image classification, accepted, IEEE Transactions on Image processing,
2015. Preprint available at arXiv:1511.03206.
2. GR Johnson, J Li, A Shariff, GK Rohde, RF Murphy, Automated Learning of
Subcellular Variation among Punctate Protein Patterns and a Generative Model of their
Relation to Microtubules, PLOS Comp. Bio, in press, 2015.
3. GR Johnson, TE Buck, DP Sullivan, GK Rohde, RF Murphy, Joint modeling of cell
and nuclear shape variation, Molecular biology of the cell 26 (22), 4046-4056, 2015.
4. JF Eisses, A Criscimanna, ZR Dionise, AI Orabi, TA Javed, S Sarwar, S Jin, L Zhou, S
Singh, M Poddar, AW Davis, AB Tosun, JA Ozolek, ME Lowe, SP Monga, GK
Rohde, F Esni, SZ Husain, Valproic acid limits pancreatic recovery following
pancreatitis by inhibiting HDACs and preventing acinar redifferentiation programs,
American Journal of Pathology, 185 (12), 3304-3315, 2015.
5. S Kolouri, AB Tosun, JA Ozolek, GK Rohde, A Continuous Linear Optimal Transport
Approach for Pattern Analysis in Image Datasets, Pattern Recognition, in press, 2015.
6. GK Rohde, Computational Analysis of Cell Images, Cytometry A, 87 (4), 294-295,
2015.
7. CM Bonfield, LM. Foley, S Kundu, W Fellows-Mayle, TK Hitchens, GK Rohde, R
Grandhi, MP Mooney, The Influence of Surgical Correction on White Matter
Microstructural Integrity in Rabbits with Familial Coronal Suture Craniosynostosis,
Neurosurgical Focus, Journal of Neurosurgery, accepted, 2015.
8. S Basu, C Liu, GK Rohde, Localizing and Extracting Filament Distributions from
Microscopy Images, Journal of Microscopy, 258(1), 13-23, 2015.
9. AB Tosun, A Yergiev, S Kolouri, J Silverman, GK Rohde, Detection of malignant
mesothelioma using nuclear structure of mesothelial cells in effusion cytology
specimens, Cytometry A, 87(4), 326-333, 2015.
10. Y Li, H Chena, GK Rohde, C Yao, L Cheng, Texton analysis for mass classification in
mammograms, Pattern Recognition Letters, 52, 87-93, 2015.
Gustavo Kunde Rohde
11. S Basu, C Liu, GK Rohde, Extraction of Individual Filaments from 2D Confocal
Microscopy Images of Flat Cells, IEEE/ACM Transactions on Computational Biology
and Bioinformatics, v12, 632-643, 2015.
12. GK Rohde, JA Ozolek, AV Parwani, L Pantanowitz, Rohde GK, Ozolek JA, Parwani
AV, Pantanowitz L. Carnegie Mellon University bioimaging day 2014: Challenges and
opportunities in digital pathology. Journal of Pathology Informatics. 2014;5:32.
doi:10.4103/2153-3539.139712.
13. J.F. Eisses, A. Davis, A.B. Tosun, Z.R. Dionise, C. Cheng, J.A. Ozolek, GK Rohde and
S.Z. Husain, A Computer-Based Automated Algorithm for Assessing Acinar Dropout
after Experimental Pancreatitis, PLOS ONE, 9(10), e110220, 2014.
14. JA Ozolek, AB Tosun, W Wang, C Chen, S Kolouri, S Basu, H Huang, GK Rohde,
Accurate diagnosis of thyroid follicular lesions from nuclear morphology using
supervised learning. Medical Image Analysis. 18(5), 772-780, 2014.
15. S. Xu, L Sun, GK Rohde, Robust efficient estimation of heart rate pulse from video.
Biomedical Optics Express 5(4), 1124-1135, 2014.
16. H Huang, AB Tosun, J Guo, C Chen, W Wang, JA Ozolek, GK Rohde, Cancer
diagnosis by nuclear morphometry using spatial information. Pattern Recognition
Letters. 42, 115-121, 2014.
17. S Basu, S Kolouri, GK Rohde, Detecting and visualizing cell phenotype differences
from microscopy images using transport-based morphometry. PNAS 111 (9), 34483453, 2014.
18. GK Rohde, F Bucholtz, JM Nichols, Maximum empirical likelihood estimation of time
delay in i.i.d. noise, IET Signal Processing, 8, pp. 720-728, 2014.
19. J Guo, H Huang, C Chen, GK Rohde, Optimized nonlinear discriminant analysis
(ONDA) for supervised pixel classification, IEEE Sig. Proc. Letters, 30:1155-1158,
2013.
20. C Cheng, W Wang, JA Ozolek, GK Rohde, A flexible and robust approach for
segmenting cell nuclei from 2D microscopy images using supervised learning and
template matching, Cytometry A, 83(5), pp. 495-507, 2013. PMC In Process.
21. S Basu, KN Dahl, GK Rohde, Localizing and extracting filament distributions from
microscopy images, Journal of Microscopy, vol. 250(1), pp 57-67, 2013. PMC3638952.
(Retracted: this article was retracted due to copyright issues relating to a few of the
microscopy images used. The paper, re-written to exclude such images is published in
ref. 8 above).
Gustavo Kunde Rohde
22. W Wang, D Slepcev, JA Ozolek, S Basu, GK Rohde, A linear optimal transportation
framework for quantifying and visualizing variations in sets of images. International
Journal of Computer Vision, vol. 101(2), pp. 254-269, 2013. PMC In Process.
23. J Li, A Shariff, GK Rohde, RF Murphy, Estimating and comparing microtubule
distributions from fluorescence microscopy images of different human cell lines. PLoS
ONE 7(11): e50292. doi:10.1371/journal.pone.0050292. PMC3508979
24. S Kustra, H Wu, S Basu, GK Rohde, CJ Bettinger, High Throughput Arrays for Rapid
Characterization of Solution Processable Transparent Conducting Electrodes, Small,
Volume 8(24), pp. 3746–3751, 2012. PMC In Process.
25. TE Buck, J Li, GK Rohde, RF Murphy, Towards the virtual cell: automated approaches
to building models of sub cellular organization 'learned' from microscopy images,
BioEssays, v. 34(9), pp.791-799, 2012. PMC3428744
26. B. Holt, H. Shams, T. Horst, S. Basu, A. Rape, Y.-L. Wang, GK Rohde, M. Mofrad,
M. Islam, K. Dahl, Altered cell mechanics from the inside: dispersed single wall carbon
nanotubes integrate with and restructure actin. J. of Functional Biomaterials, vol. 3(2),
pp. 398-417, 2012.
27. W Wang, Y Mo, JA Ozolek, GK Rohde, Penalized Fisher Discriminant Analysis and
Its Application to Image Based Morphometry, Pattern Recognition Letters, 32(15):
2128-2135, 2011. PMC3225900
28. S Choi, W Wang, AJS Ribeiro, A Kalinowski, SQ Gregg, PL Opreski, LJ Niedemhofer,
GK Rohde, KN Dahl, Computational image analysis of nuclear morphology associated
with various nuclear specific aging disorders. Nucleus, vol. 2(6), pp. 570-579, 2011.
PMC3324345
29. C Chen, JA Ozolek, W Wang, GK Rohde, A General System for Automatic
Biomedical Image Segmentation using Intensity neighborhoods, International Journal of
Biomedical Imaging, vol. 2011, Article ID 606857, 12 pages, 2011.
doi:10.1155/2011/606857. PMC3132524.
30. W Wang, JA Ozolek, D Slepcev, AB Lee, C Chen, GK Rohde, An optimal
transportation approach for nuclear structure-based pathology, IEEE Transactions on
Medical Imaging, 30, pp. 621-631, 2011. PMC3418065.
31. W Wang, JA Ozolek, GK Rohde, Detection and classification of thyroid follicular
lesions based on nuclear structure from histopathology images. Cytometry vol 77A, pp.
485-494, 2010. PMC3010854.
32. A Shari , RF Murphy, GK Rohde, A generative model of microtubule distributions,
and indirect estimation of its parameters from fluorescence microscopy images.
Cytometry vol 77A, pp. 457-466, 2010. PMC2901542.
Gustavo Kunde Rohde
33. GK Rohde, A Aldroubi, DM Healy, Jr., Interpolation artifacts in sub-pixel image
registration. IEEE Trans. Image Processing, 18(2): 333-345, 2009.
34. GK Rohde, AJS Ribeiro, KN Dahl, RF Murphy, Deformation-based nuclear
morphometry: capturing nuclear shape variation in HeLa cells. Cytometry, vol 73A, pp.
341-350, 2008.
35. GK Rohde, JM Nichols, F Bucholtz, Chaotic signal detection and estimation based on
attractor sets: applications to secure communications. Chaos, vol 18, pp. 013114, 2008.
36. GK Rohde, JM Nichols, DM Dissinger, F Bucholtz, Stochastic analysis of recurrence
plots with applications to the detection of deterministic signals. Physica D, vol. 237, pp.
619-629, 2008.
37. DP Waber, C De Moor, PW Forbes, CR Almli, KN Botteron, G Leonard, D Milovan, T
Paus, J Rumsey, and the Brain Development Cooperative Group. The NIH MRI
study of normal brain development: Performance of a population based sample of
healthy children aged 6 to 18 years on a neuropsychological battery. Journal of the
International Neuropsychological Society 13:1-18, 2007.
38. CR Almli, MJ Rivkin, RC McKinstry, and the Brain Development Cooperative
Group. The NIH MRI study of normal brain development (Objective-2): Newborns,
infants, toddlers, and preschoolers. NeuroImage 35:308-325, 2007.
39. A Evans, and the Brain Development Cooperative Group. The NIH MRI study of
normal brain development. NeuroImage 30:184-202, 2006.
40. S Marenco, R Rawlings, GK Rohde, AS Barnett, RA Honea, C Pierpaoli, DR
Weinberger, Regional distribution of measurement error in diffusion tensor imaging.
Psychiatry Res, Jun 30;147(1):69-78, 2006.
41. GK Rohde, AS Barnett, PJ Basser, C Pierpaoli, Estimating intensity variance due to
noise in registered images: applications to diffusion tensor MRI. Neuroimage, v. 26(3),
pp. 673-84, 2005.
42. GK Rohde, BM Dawant, S-F Lin, Correction of motion artifact in cardiac optical
mapping using image registration. IEEE Trans Biomed Eng, v. 52(2), pp. 338-41, 2005.
43. Y Assaf, RZ Freidlin, GK Rohde, PJ Basser, New modeling and experimental
framework to characterize hindered and restricted water diffusion in brain white matter.
Magn Reson Med., Nov;52(5):965-78, 2004.
44. GK Rohde, AS Barnet, PJ Basser, S Marenco, C Pierpaoli, Comprehensive approach
for correction of motion and distortion in diffusion-weighted MRI. Magn Reson Med.,
Jan;51(1):103-14, 2004.
Gustavo Kunde Rohde
45. GK Rohde, A Aldroubi, BM Dawant, The adaptive bases algorithm for intensity-based
nonrigid image registration. IEEE Trans Med Imaging, Nov;22(11):1470-9, 2003.
Peer-reviewed Conference Publications
1. S Kolouri, GK Rohde, Transport-based single frame super resolution of very low
resolution face images. IEEE CVPR 2015, pp 4876-4884.
2. S Kolouri, D Slepcev, GK Rohde, A symmetric deformation-based similarity measure
for shape analysis. IEEE ISBI 2015, pp 314-318.
3. S Kolouri, S Basu, GK Rohde, Learning and visualizing statistical relationships
between protein distributions from microscopy images. IEEE ISBI 2014, pp. 381-384.
4. GK Rohde, New methods for quantifying and visualizing information from images of
cells: An overview. Conf Proc IEEE Eng Med Biol Soc. 2013 Jul;2013:121-4. doi:
10.1109/EMBC.2013.6609452.
5. C Chen, W Wang, JA Ozolek, N Lages, SJ Altschuler, LF Wu, GK Rohde, A template
matching approach for segmenting microscopy images, Proceedings of the IEEE
International Symposium on Biomedical Imaging (ISBI 2012), pp. 768-771.
6. A Shari , RF Murphy, GK Rohde, Automated estimation of microtubule model
parameters from 3-D live cell microscopy images, Proceedings of the IEEE
International Symposium on Biomedical Imaging (ISBI 2011), pp. 1330-1333.
7. W Wang, Y Mo, JA Ozolek, GK Rohde, Characterizing morphology di erences from
image data using a modified Fisher criterion, Proceedings of the IEEE International
Symposium on Biomedical Imaging (ISBI 2011), pp. 129-132.
8. C Cheng, JA Ozolek, W Wang, GK Rohde, A pixel classification system for
segmenting biomedical images using intensity neighborhoods and dimension reduction,
Proceedings of the IEEE International Symposium on Biomedical Imaging (ISBI 2011),
pp. 1649-1652.
9. W Wang, C Chen, T Peng, D Slepcev, JA Ozolek, GK Rohde, A graph-based method
for detecting characteristic phenotypes from biomedical images. Proceedings of the
IEEE International Symposium on Biomedical Imaging (ISBI 2010), pp. 129-132, 2010.
10. T Peng, W Wang, GK Rohde, RF Murphy, Instance-based generative biological shape
modeling. Proceedings of the IEEE International Symposium on Biomedical Imaging
(ISBI 2009), pp. 690-693, 2009.
11. A Shari , GK Rohde, and RF Murphy, Indirect learning of generative models for
microtubule distribution from fluorescence microscope images. Proceedings of the
Gustavo Kunde Rohde
ICML-UAI-COLT 2009 Workshop on Automated Interpretation and Modeling of Cell
Images (Cell-Image Learning 2009), 2009.
12. GK Rohde, W Wang, T Peng, RF Murphy, Deformation-based nonlinear dimension
reduction: applications to nuclear morphometry. Proceedings of the IEEE International
Symposium on Biomedical Imaging (ISBI 2008), pp. 500-503, 2008.
13. C Hallock, I Ozgunes, R Bhagavatula, GK Rohde, JC Crowley, CE Onorato, A
Mavalankar, A Chebira, CH Tan, M Puschel and J Kovacevic, Axonal bouton
modeling, detection and distribution analysis for the study of neural circuit organization
and plasticity, Proceedings of the IEEE International Symposium on Biomedical
Imaging (ISBI 2008), pp 165-168, 2008.
14. A Chebira, JA Ozolek , CA Castro, WG Jenkinson, M Gore, R Bhagavatula, I
Khaimovich, Ormon, CS Navara, M Sukhwani, KE Orwig, A Ben-Yehudah, G
Schatten, GK Rohde, J Kovacevic, Multiresolution identification of germ layer
components in teratomas derived from human, nonhuman primate, and murine
embryonic stem cells, Proceedings of the IEEE International Symposium on Biomedical
Imaging (ISBI 2008), pp.979-982, 2008.
15. DM Healy, Jr., GK Rohde, Fast global image registration using random projections.
Proceedings of the IEEE Int. Simp. on Biomedical Imaging, pp. 648-651, 2007.
16. GK Rohde, DM Healy, Jr., CA Berenstein, A Aldroubi, Interpolation artifacts in
biomedical image registration. Proceedings of the IEEE Int. Simp. on Biomedical
Imaging, pp. 476-479, 2007.
17. GK Rohde, DM Healy, Jr., CA Berenstein, A Aldroubi, Measuring image similarity to
sub-pixel accuracy, Proceedings of the IEEE Int. Simp. on Biomedical Imaging, pp.
638-641, 2006.
18. GK Rohde, DM Healy, Jr., CA Berenstein, A Aldroubi, D Rockmore, Stochastic
analysis of geometric image processing using B-splines, Proceedings of IEEE ICASSP,
pp. 1017-1020, 2006. (Invited)
19. GK Rohde, S Pajevic, C Pierpaoli, Multi-channel registration of di usion tensor
images using directional information. Proceedings of the IEEE Int. Simp. on
Biomedical Imaging, pp. 712-715, 2004.
20. GK Rohde, S Pajevic, C Pierpaoli, PJ Basser, A comprehensive approach for multichannel image registration. Proceedings of the Second International Workshop on
Biomedical Image registraion (WBIR03), pp. 214-223, 2003.
Gustavo Kunde Rohde
Conference publications and abstracts
1. S Kolouri, GK Rohde, PCA-Based Super-Resolution in Transport Space,
Computational Optical Sensing and Imaging, CTh3E. 2, 2015.
2. AB Tosun, O Yergiyev, S Kolouri, JF Silverman, GK Rohde, Novel computer-aided
diagnosis of mesothelioma using nuclear structure of mesothelial cells in effusion
cytology specimens, SPIE Medical Imaging, 90410Z-90410Z-6, 2014.
3. S Kolouri, GK Rohde, Quantifying and visualizing variations in sets of images using
continuous linear optimal transport, SPIE Medical Imaging, 903438-903438-6, 2014.
4. O Yergiyev, AB Tosun, GK Rohde, JF Silverman, A Novel Computerized Image
Analysis Method to Differentiate Malignant Mesothelioma from Reactive Mesothelial
Proliferations in Effusion Cytology Specimens, Laboratory Investigation, 94, 533A533A, 2014.
5. S Kolouri, GK Rohde, Temporal information inference from static high-content
fluorescent microscopy, Northeast Bioengineering Conference (NEBEC), 2014 40th
Annual, 1-2.
6. JF Eisses, A Davis, AB Tosun, ZR Dionise, C Cheng, J Guo, JA Ozolek, GK Rohde,
SZ Husain, A Rapid Computer-Based Automated Algorithm for Assessing Acinar
Dropout After Experimental Pancreatitis, PANCREAS 42 (8), 1348-1348, 2013.
7. GK Rohde, New methods for quantifying and visualizing information from images of
cells: an overview, accepted, IEEE-EMBS, Osaka, Japan, 2013.
8. GK Rohde, W. Wang, S. Basu, D. Slepcev, A linear transport-based embedding
method for analyzing biomedical imaging, Asilomar conference on signals, systems,
and computers, pp. 1593-1596, 2012.
9. C. Chen, J. A. Ozolek, W. Wang, GK Rohde, An improved method for segmenting cell
nuclei from microscopy images. CYTO 2012.
10. GK Rohde, W. Wang, J. A. Ozolek, D. Slepcev, A new method for visualizing
difference sin cell morphology. CYTO 2012.
11. GK Rohde, K. Dahl, S. Basu, A new accurate method for detecting subcellular filament
structures from image data. CYTO 2012.
Gustavo Kunde Rohde
12. C Pierpaoli, L Walker, MO Irfanoglu, A Barnett, P Basser, LC Chang, C Koay, S
Pajevic, GK Rohde, J Sarlls, M Wu, TORTOISE: an integrated software package for
processing of diffusion MRI data, ISMRM 2010, Vol 18, P. 1597, 2010.
13. GK Rohde, W. Wang, D. Slepcev, A. B. Lee, C. Chen, J. A. Ozolek, Detecting and
classify¬ing cancers from image data using optimal transportation, 26th, Southern
Biomedical Engineering Concerence, K. E. Herold, W. E. Bentley, J. Vossoughi (Eds.),
pp. 353-356, 2010. (invited)
14. W. Wang, J.A. Ozolek, D. Slepcev, GK Rohde, Geometric approaches for cancer
detection and classification based on nuclear structure, APIII 2009.
15. W. Wang, J. Ozolek, GK Rohde, Geometry Based Nuclear Morphometry for
Hepatoblastoma, 2009 BMES Annual Fall Scientific Meeting, Pittsburgh, PA. October
7-10.
16. R. Bhagavatula, I. Ozgunes, N. Marthaler, C. Onorato, J. Crowley, GK Rohde, and J.
Kovacevic, ”Automated Detection of Axonal Boutons in Large Three-Dimensional
Neuroanatomical Data Sets”, BMES Annual Fall Meeting, Pittsburgh, PA, Oct. 2009.
17. Ozgunes, R. Bhagavatula, N. E. Marthaler, C. E. Onorato, J. Kovacevic, GK Rohde, J.
C. Crowley (2009) Automated detection of axonal boutons in neuroanatomical image
datasets. Program No. 104.17. Neuroscience Meeting Planner. Chicago, IL: Society for
Neuroscience, 2009. Online.
18. A Shariff, RF Murphy, GK Rohde, Estimating Microtubule Distributions in Live Cells
from Confocal Microscopy Images. 2009 BMES Annual Fall Scientific Meeting,
Pittsburgh, PA. October 7-10.
19. Chen, J. Ozolek, C. Castro, P. Mills, GK Rohde, Relating MRI to Histology Through
Machine Learning, 2009 BMES Annual Fall Scientific Meeting, Pittsburgh, PA.
October 7-10.
20. A Shariff, GK Rohde, R. F. Murphy R. F. Indirect learning of generative models for
micro¬tubule distribution from fluorescence microscope images. 2009 Cold Spring
Harbor meeting on Computational Cell Biology, Cold Spring Harbor, NY. March 24 27, 2009.
21. GK Rohde, D.M. Healy, Jr., A. Aldroubi, Sampling and reconstruction for biomedical
image registration. Proc. 41st Annual Asilomar Conference on Signals, Systems, and
Computers, Pacific Grove, CA. pp 220-223, 2007(invited).
22. GK Rohde, J.M. Nichols, F. Bucholtz, J.V. Michalowicz, Signal estimation based on
mutual infor¬mation maximization. Proc. 41st Annual Asilomar Conference on Signals,
Systems, and Computers, Pacific Grove, CA., 2007.
Gustavo Kunde Rohde
23. J. S. Ribeiro, GK Rohde, P. J. Sammak, J. Yue, K. N. Dahl. Time-Dependent
Morphological Dynamics of the Cell Nucleus During Lamin A/C Knockdown. BMES,
Los Angeles, September 2007.
24. J. S. Ribeiro, J. T. Philip, GK Rohde, P. J. Sammak, J. Yue, K. N. Dahl, TimeDependent Morphological Dynamics of Cell Nuclei During Altered Lamin A/C
Expression, Engineering in Cell Biology II, Boston, MA August 2007.
25. J.B. West, C.R. Maurer, Jr., J.R. Dooley, GK Rohde, Deformable registration of
abdominal CT images: Tissue sti nes constraints using B-splines. Proc. SPIE Vol.
6144, p. 289-296, Medical Imaging 2006: Image Processing; Joseph M. Reinhardt,
Josien P. Pluim; Eds.
26. GK Rohde, D.M. Healy Jr., C.A. Berenstein, Measuring image similarity in the
presence of noise. In Proceedings of the SPIE Medical Imaging: Image Processing. San
Diego, February 2005. Editors: J.M. Fitzpatrick and J.M. Reinhardt. SPIE Press, 2005,
vol. 5747, p. 132-143.
27. GK Rohde, A.S. Barnett, P.J. Basser, C. Pierpaoli, Estimating noise variance in
registered images. Proceeding of the SPIE Medical Imaging: Image Processing. San
Diego, February 2005. Editors: J.M. Fitzpatrick and J.M. Reinhardt. SPIE Press, 2005,
vol. 5747, p. 655-666.
28. L.-C. Chang, GK Rohde, C. Pierpaoli, An automatic method for estimating noiseinduced signal variance in magnitude reconstructed magnetic resonance images. Proc.
SPIE. Medical Imaging: Image Processing. Proceeding of the SPIE Medical Imaging:
Image Processing. San Diego, February 2005. Editors: J.M. Fitzpatrick and J.M.
Reinhardt. SPIE Press, 2005, vol. 5747, p. 1136-1142.
29. L.-C Chang, GK Rohde, P. J. Basser, Analytic expressions for the uncertainty of DTIderived parameters and their validation using monte carlo methods. ISMRM, March
2005, Alberta, Canada.
30. GK Rohde, S. Pajevic, C. Pierpaoli, Nonlinear registration of di usion tensor images
using directional information. ISMRM, May 2004, Kyoto, Japan. Pp 1213.
31. S. Pajevic, GK Rohde, P.J. Basser, A. Aldroubi, Non-homogeneous Wavelet
Denoising. ISMRM, May 2004, Kyoto, Japan. Pp 2223.
32. L-C. Chang, GK Rohde, D.K. Jones, P.J. Basser, C. Pierpaoli. RESTORE: Robust
estimation of tensors by outlier rejection. ISMRM, May 2004, Kyoto, Japan. Pp. 1223.
33. Y. Assaf, R.Z. Freidlin, GK Rohde, P.J. Basser, A new modeling and experimental
framework to characterize hindered and restricted water di usion in brain white matter.
ISMRM, May 2004, Kyoto, Japan. Pp. 251.
Gustavo Kunde Rohde
34. GK Rohde, A.S. Barnett, P.J. Basser, S. Marenco, C. Pierpaoli. A comprehensive
approach for correcting motion and distortion in di usion weighted MRI. Proc. of 11th
ISMRM, Toronto, Canada. July 2003. Pp 1055.
35. GK Rohde, S. Pajevic, C. Pierpaoli, P.J. Basser. Covariance matrix based elastic multichannel image registration. Proc. of 11th ISMRM, Toronto, Canada. July 2003. Pp 615.
36. C. Pierpaoli, S. Marenco, GK Rohde, D.K. Jones, A.S. Barnett. Analyzing the
contribution of caridac pulsation to the variability of quantities derived from the
di usion tensor. Proc. of the 11th ISMRM, Toronto, Canada. July 2003. Pp. 70.
37. GK Rohde, A.S. Barnett, P.J. Basser, S. Marenco, C. Pierpaoli. A comprehensive
approach for correcting motion and distortion in di usion weighted MRI. Proceedings
of the Twenty First Southern Biomedical Engineering Conference, Sept. 28-19, 2002.
Bethesda, Maryland, USA. Pp. 205-206.
38. GK Rohde, V. Sidorov, A. Aldroubi, B.M. Dawant, S.-F. Lin. Correction of Motion
Artifact in Cardiac Optical Mapping Using Image Registration Technique. IEEE/EMBS
2002 ,Houston, TX., USA. October 2002.
39. GK Rohde, C. Pierpaoli, S. Pajevic, and P.J. Basser. Information theoretic matching of
non-scalar images. ISMRM 2002, Hawaii, USA. Pp. 2483.
40. S. Pajevic, P.J. Basser, GK Rohde, C. Pierpaoli, D.K. Jones, A. Aldroubi. Multiscale
Approaches for Di usion Tensor MRI. ISMRM 2002, Hawaii, USA. Pp. 1176.
41. GK Rohde, A. Aldroubi, B. Dawant. The adaptive bases algorithm for nonrigid image
registra¬tion. Proc. SPIE Vol. 4684, p. 933-944. Medical Imaging 2002: Image
Processing. Milan Sonka; Kenneth M. Hanson; Eds.
42. GK Rohde, A. Aldroubi, B. Dawant. Adaptive free-form deformation for interpatient
medical image registration. Proc. SPIE Vol. 4322, p. 1578-1587. Medical Imaging
2001: Image Processing. Milan Sonka; Kenneth M. Hanson; Eds.
43. T. Disenbacher, GK Rohde, D.P. Harding, A. Aldroubi, B. Dawant. Multiscale
nonrigid data registration using adaptive basis functions. Proc. SPIE Vol. 4119, p. 10761083, Wavelet Appli¬cations in Signal and Image Processing VIII 2000, Akram
Aldroubi; Andrew F. Laine; Michael A. Unser; Eds.
44. S.-F. Lin, GK Rohde, A. Aldroubi. Wavelet denoising of epicardial fluorescence
imaging. Proc. SPIE Vol. 3458, p. 267-273, Wavelet Applications in Signal and
Imaging Processing VI 1998, Andrew F. Laine; Michael A. Unser; Akram Aldroubi;
Eds.
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