- Google scholar (generaly more up to date than the list below)
Selected publications
- S Kolouri, SR Park, M Thorpe, D Slepcev, GK Rohde, Optimal mass transport for signal processing and machine learning, IEEE Signal Processing Magazine, 34(4), pp 43-59, 2017. Journal , code
- S Kundu, S Kolouri, KI Erickson, AF Kramer, E McAuley, GK Rohde, Discovery and visualization of structural biomarkers from MRI using transport-based morphometry, in press, Neuroimage, 2017. arXiv preprint arXiv:1705.04919: preprint
- JM Nichols, AT Watnik, T Doster, S Park, A Kanaev, L Cattell, GK Rohde, An optimal transport model for imaging in atmospheric turbulence, arXiv preprint arXiv:1705.01050, 2017. preprint .
- SR Park, S Kolouri, S Kundu, GK Rohde, The Cumulative Distribution Transform and Linear Pattern Classification, in press, Applied and Computational Harmonic Anaysis, 2017. arXiv preprint arXiv:1507.05936. link Python software , Matlab software .
- M Hanna, C Liu, GK Rohde, R Singh, Predictive nuclear chromatin characteristics of melanoma and dysplastic nevi, Journal of Pathology Informatics 2017, Apr 10;8:15. Journal site , pubmed .
- Y Huang, H Zheng, X Ding, GK Rohde, Epithelium-stroma classification via deep neural networks and domain adaptation in histopathological images, in Press. IEEE J. Biomed Health Informatics, 2017. journal
- M Thorpe, SR Park, S Kolouri, GK Rohde, D Slepcev, A Transportation $ L^ p $ Distance for Signal Analysis, J. Mathematical Imaging and Vision, 59 (2), pp. 187-210, 2017, arXiv:1609.08669. paper , code (warning ~2GB)
- S Kolouri, S Park, M Thorpe, D Slepcev, GK Rohde, Transport-based analysis, modeling, and learning from signal and data distributions, 2016, arXiv preprint arXiv:1609.04767. link , code
- C Liu, F Shang, JA Ozolek, GK Rohde, Detecting and Segmenting Cell Nuclei in 2D Microscopy Images. In Press, Journal of Pathology Informatics, 2016; 7:42. journal , software (warning, ~1GB)
- Y Huang, C Liu, JF Eisses, SZ Husain, GK Rohde, A supervised learning framework for pancreatic islet semgmentation with mult-scal clore-texture features and rolling guidance filters. Cytometry A, 89(10), pp. 893-902, 2016. paper
- S Kolouri, Y Zou, GK Rohde, Sliced Wasserstein Kernels for Probability Distributions, arXiv:1511.03198. CVPR 2016. link , software
- S Kolouri, SR Park, GK Rohde, The Radon cumulative distribution transform and its application to image classification, IEEE Transactions on Image Processing, 25(2), pp 920-934, 2016. Preprint available at arXiv:1511.03206. link , Matlab software , iPython notebook example
- S Kolouri, AB Tosun, JA Ozolek, GK Rohde, A Continuous Linear Optimal Transport Approach for Pattern Analysis in Image Datasets, Pattern Recognition, 2016. preprint , journal site .
- 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. Biol, 2015. link , code
- 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, 2015. paper
- GR Johnson, TE Buck, DP Sullivan, GK Rohde, RF Murphy, Joint Modeling of Cell and Nuclear Shape Variation, Molecular Biology of the Cell, mbc. E15-06-0370, in press, 2015. Journal site , code .
- S Kolouri, GK Rohde, Transport-based single frame super resolution of very low resolution face images. IEEE CVPR 2015, pp 4876-4884. pdf
- GK Rohde, Computational Analysis of Cell Images, Cytometry A, 87 (4), 294-295, 2015. pdf
- 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. pubmed
- 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. pdf
- S Basu, C Liu, GK Rohde, Localizing and Extracting Filament Distributions from Microscopy Images, Localizing and Extracting Filament Distributions from Microscopy Images, Journal of Microscopy, 258(1), 13-23, 2015. html
- 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.
- Y Li, H Chena, GK Rohde, C Yao, L Cheng, Texton analysis for mass classification in mammograms, Texton analysis for mass classification in mammograms, Pattern Recognition Letters, 52, 87-93, 2015. html
- J.F. Eisses, A. Davis, A.B. Tosun, Z.R. Dionise, C. Cheng, J.A. Ozolek, G.K. Rohde and S.Z. Husain, A Computer-Based Automated Algorithm for Assessing Acinar Dropout after Experimental Pancreatitis, PLOS ONE, 9(10), e110220, 2014. html , software
- S Kolouri, S Basu, GK Rohde, Learning and visualizing statistical relationships betwen protein distributions from microscopy images. Accepted, IEEE ISBI 2014, pp 381-384.
- GK Rohde, JA Ozolek, AV Parwani, L Pantanowitz, CMU Bioimaging Day 2014: Challenges and Opportunities in Digital Pathology. J. Pathol. Informatics. 2014; in press. html
- 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. link
- S. Xu, L Sun, GK Rohde, Robust efficient estimation of heart rate pulse from video. Biomedical Optics Express 5(4), 1124-1135, 2014. link
- 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. (pdf)
- S. Basu, S. Kolouri, GK Rohde, Detecting and visualizing
cell phenotype differences from microscopy images using transport-based
morphometry. PNAS 111 (9), 3448-3453, 2014. pdf , publisher , software
- GK Rohde, F Buchotz, JM Nichols, Maximum empirical likelihood estimation of time delay in i.i.d. noise, IET Signal Processing, 8, pp. 720-728, 2014.. (pdf)
- J. Guo, H. Huang, C. Chen, G.K. Rohde, Optimized nonlinear
discriminant analysis (ONDA) for supervised pixel classification, IEEE
Sig. Proc. Letters, 30:1155-1158, 2013.
(pdf) , supplement
- C. Cheng, W. Wang, J. A. Ozolek, G. K. 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.
Journal site , pdf , software .
- W. Wang, D. Slepcev, J. A. Ozolek, S. Basu, G. K. 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. Journal
site , pdf .
- J. Li, A. Shariff, G.K. Rohde, R. F. 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, 2012.
(html)
- S. Kustra, H. Wu, S. Basu, G.K. Rohde, C. J. Bettinger,
High Throughput Arrays for Rapid Characterization of Solution
Processable Transparent Conducting Electrodes, Small, Volume 8(24), pp.
3746-3751, 2012.
- C. Chen, W. Wang, J.A. Ozolek, N. Lages, S.J. Altschuler,
L.F. Wu, G.K. Rohde, A template matching approach for segmenting
microscopy images, Proceedings of the IEEE International Symposium on
Biomedical Imaging (ISBI 2012), pp. 768-771
- T. E. Buck, J. Li, G. K. Rohde, R. F. Murphy, Towards the
virtual cell: automated approaches to building models of subcellular
organization `learned' from microscopy images. BioEssays,
34(9):791-799, 2012.
- B. Holt, H. Shams, T. Horst, S. Basu, A. Rape, Y.-L. Wang,
G. K. 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, 3(2), pp. 398-417,
2012.
- W. Wang, Y. Mo, J. A. Ozolek, G. K. Rohde, Penalized
Fisher discriminant analysis and its application to image-based
morphometry. Pattern Recognition Letters, 32(15): 2128-2135, 2011. (pdf)
- S. Choi, W. Wang, A. J. S. Ribeiro, A. Kalinowski, S. Q.
Gregg, P. L. Opreski, L. J. Niedemhofer, G. K. Rohde, K. N. Dahl,
Computational image analysis of nuclear morphology associated with
various nuclear specific aging disorders. Nucleus, 2011.
(link)
- C. Chen, J. A. Ozolek, W. Wang, G. K. Rohde, A general
system for automatic biomedical image segmentation using intensity
neighborhoods, International Journal of Biomedical Imaging, Volume
2011, Article ID 606857. (link)
- W. Wang, J. A. Ozolek, D. Slepcev, A. B. Lee, C. Chen, G.
K. Rohde, An optimal transportation approach for nuclear
structure-based pathology, IEEE Transactions on Medical Imaging, 30,
pp. 621-631, 2011. (pdf)
- A. Shariff, R. F. Murphy, G. K. 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, p. 1330-1333. (pdf)
- W. Wang, Y. Mo, J. A. Ozolek, G. K. Rohde, Characterizing
morphology differences from image data using a modified fisher
criterion, Proceedings of the IEEE International Symposium on
Biomedical Imaging (ISBI), 2011, p. 129-132. (pdf)
- C. Chen, J. A. Ozolek, W. Wang, G.K. Rohde, A pixel
classification system for segmenting biomedical images intensity
neighborhoods and dimension reduction, Proceedings of the IEEE
International Symposium on Biomedical Imaging (ISBI), 2011, p.
1649-1652. (pdf)
- W. Wang, J. A. Ozolek, G.K. Rohde, Detection and
classification of thyroid follicular lesions based on nuclear structure
from histopathology images. Cytometry 77A, pp. 485-494, 2010. (reprint)
- W. Wang, C. Chen, T. Peng, D. Slepcev, J. A. Ozolek, G. K.
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 (pdf) .
- A. Shariff, R. F. Murphy, G. K. Rohde, A generative model
of microtubule distributions, and indirect estimation of its parameters
from fluorescence microscopy images. Cytometry 77A, pp. 457-466, 2010. (reprint)
- G. K. Rohde, A. Aldroubi, D. M. Healy, Jr., Interpolation
Artifacts in Sub-Pixel Image Registration. IEEE Transactions on Image
Processing 18(2), pp. 333-345, 2009. (preprint)
- T. Peng, W. Wang, G.K. Rohde, R. F. Murphy, Instance-based
generative biological shape modeling. Proceedings of the IEEE
International Symposium on Biomedical Imaging (ISBI 2009), pp. 690-693,
2009 (pdf) .
- G.K. Rohde, J.M. Nichols, B.M. Dissinger, F. Bucholtz,
Stochasic analysis of recurrence plots with applications to the
detection of deterministic signals. Physica D, vol 237, pp. 619-629,
2008. (preprint)
- G.K. Rohde, A.J.S. Ribeiro, K.N. Dahl, R.F. Murphy,
Deformation-based nuclear morphometry: Capturing nuclear shape
variation in HeLa cells. Cytometry, vol 73A, pp. 341-350, 2008. (pdf)
- G.K. Rohde, W. Wang, T. Peng, R.F. Murphy,
Deformation-based nonlinear dimension reduction: applications to
nuclear morphometry. Proceedings of the IEEE Int. Simp. on Biomedical
Imaging, pp. 500-503, 2008. (pdf)
- C.A. Hallock, I. Ozgunes, R. Bhagavatula, G.K. Rohde, J.C.
Crowley, C.E. Onorato, A. Mavalankar, A. Chebira, Chuen Hwa Tan, M.
Puschel, J. Kovacevic, Axonal bouton modeling, detection and
distribution analysis for the study of neural circuit organization and
plasticity. Proceedings of the IEEE Int. Simp. on Biomedical Imaging,
pp. 165-168, 2008. (pdf)
- A. Chebira, J.A. Ozolek , C. A. Castro, W.G. Jenkinson, M.
Gore, R. Bhagavatula, I. Khaimovich, S.E. Ormon, C.S. Navara, M.
Sukhwani, K.E. Orwig, A. Ben-Yehudah, G. Schatten, G.K. 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 Int. Simp. on Biomedical Imaging,
pp. 979-982, 2008. (pdf)
- G.K. Rohde, J.M. Nichols, F. Bucholtz, Chaotic signal
detection and estimation based on attractor sets: Applications to
secure communications. Chaos, vol 18, pp. 013114, 2008. (pdf)
- G.K. Rohde, D.M. Healy, Jr., A. Aldroubi, Sampling and
reconstruction for biomedical image registration. Proceedings of the
Forty-First IEEE Asilomar Conference on Signals, Systems &
Computers, pp. 220-223, 2007. (pdf)
- G.K. Rohde, D.M. Healy, Jr., C.A. Berenstein, A. Aldroubi,
Interpolation artifacts in biomedical image registration, Proceedings
of the IEEE Int. Simp. on Biomedical Imaging, pp. 648-651, 2007. (pdf)
- D.M. Healy, Jr., G.K. Rohde, Fast global image
registration using random projections, Proceedings of the IEEE Int.
Simp. on Biomedical Imaging, pp. 476-479, 2007. (pdf)
- G.K. Rohde, D.M. Healy, Jr., C.A. Berenstein, A. Aldroubi,
Measuring image similarity to sub-pixel accuracy, Proceedings of the
IEEE Int. Simp. on Biomedical Imaging, pp. 638-641, 2006. (pdf)
- G.K. Rohde, D.M. Healy, Jr., C.A. Berenstein, A. Aldroubi,
D. Rockmore, Stochastic analysis of geometric image processing using
B-splines, Proceedings of IEEE ICASSP, pp. 1017-1020, 2006. (pdf)
- G.K. Rohde, A.S. Barnett, P.J. Basser, C. Pierpaoli,
Estimating intensity variance due to noise in registered images:
applications to DT-MRI. Neuroimage, vol. 26, pp. 673-684, 2005. (pdf)
- G.K. Rohde, C.A. Berenstein, D.M. Healy, Jr., Measuring
image similarity in the presence of noise. Proceedings of the SPIE,
vol. 5747, Medical Imaging 2005: Image Processing; pp. 132-143, 2005. (pdf)
- G.K. Rohde, B.M. Dawant, S.-F Lin, Correction of motion
artifact in cardiac optical mapping using image registration. IEEE
Transactions on Biomedical Engineering, vol. 52, pp. 338-341, 2005. (pdf)
- G.K. Rohde, A.S. Barnet, P.J. Basser, S. Marenco, C.
Pierpaoli, Comprehensive approach for motion and distortion correction
in diffusion weighted MRI. Magnetic Resonance in Medicine, vol. 51, pp.
103-114, 2004. (pdf)
- G.K. Rohde, A. Aldroubi, B.M. Dawant, The adaptive bases
algorithm for intensity based nonrigid image registration. Special
issue on image registration. IEEE Transactions on Medical Imaging, vol.
22, pp. 1470-1479, 2003. (pdf)
- G.K. Rohde, S. Pajevic, C. Pierpaoli, P.J. Basser. A
comprehensive approach for multi-channel image registration. Second
International Workshop on Biomedical Image registration (WBIR03),
Philadelphia, Pennsylvania. June 2003. Pp. 214-223. (pdf)