Joanna Klukowska
"Everything should be made as simple as possible, but not one bit simpler." -- Einstein (attributed).
Clinical Associate Professor
Computer Science Department,
Courant Institute of Mathematical Sciences,
New York University
Warren Weaver Hall, Room 423
251 Mercer Street
New York, NY 10012
(212) 998 3146
Older Research and Publications
I received my doctorate in Computer Science in September 2013 under the guidance of Distinguished Professor Gabor T. Herman of The Graduate Center of the City University of New York. My dissertation topic was the development of correction methods that deblur images obtained by electron and soft x-ray microscopes.
The following publications were result of that work.
Refereed Articles
Joaquín Otón, Eva Pereiro, José J. Conesa, Francisco J. Chichón, Daniel Luque, Javier M. Rodríguez, Ana J. Pérez-Berná, Carlos Oscar S. Sorzano, Joanna Klukowska, Gabor T. Herman, Javier Vargas, Roberto Marabini, José L. Carrascosa, José M. Carazo, XTEND: Extending the depth of field in cryo soft X-ray tomography, Nature Scientific Reports, Volume 7, id. 45808 (2017), See online.
Joanna Klukowska, Gabor T. Herman, Joaquin Oton, Roberto Marabini, Jose-Maria Carazo, The Soft X-Ray Transform, Inverse Problems 30 125015, 2014, See online.
Garrett Katz, Younes Benkarroum, Hui Wei, William J. Rice, Doris Bucher, Alexandra Alimova, Al Katz, Joanna Klukowska, Gabor T. Herman and Paul Gottlieb, Morphology of Influenza B/Lee/40 Determined by Cryo-Electron Microscopy, PLoS ONE, 9(2):e88288, 2014, See online.
Joanna Klukowska, Gabor T. Herman, Reconstruction From Microscopic Projections with Defocus-Gradient and Attenuation Effects in Computational Methods for Three-Dimensional Microscopy Reconstruction. In: Herman GT, Frank J (eds) Computational Methods for Three-Dimensional Microscopy Reconstruction, Springer, 2014.
Joanna Klukowska, Ran Davidi, Gabor T. Herman, SNARK09 - A software package for reconstruction of 2D images from 1D projections, Computer Methods and Programs in Biomedicine, 110:424-440, 2013, PMID: 23414602, PubMed Journal website.
Ivan G. Kazantsev, Joanna Klukowska, Gabor T. Herman, Laslo Cernetic, Fully three-dimensional defocus-gradient corrected backprojection in cryoelectron microscopy, Ultramicroscopy,110:1128-1142, 2010, PMID: 20462697, PMCID: PMC2912958, PubMed, Journal website.
Joanna Klukowska, Gabor T.Herman, Ivan G.Kazantsev, Correction of Distance-Dependent Blurring in Projection Data for Fully Three-Dimensional Electron Microscopic Reconstruction, In IEEE International Symposium on Biomedical Imaging: From Nano to Macro, pages 1117–1120, 2010. Conference Website, IEEE Xplore.
Amotz Bar-Noy, Joanna Klukowska, Finding Mobile Data: Efficiency vs. Location Inaccuracy, 15th Annual European Symposium on Algorithms, Eilat, Israel, October 8-10, 2007. Conference Website, Springer
Presentations at Workshops and Conferences (Peer Reviewed)
Joanna Klukowska, Gabor T. Herman, Replication Artifact in Data Collected by Soft X-ray Microscopy, IEEE Signal Processing in Medicine and Biology Symposium, Polytechnic Institute of New York University , December 7, 2013.
Joanna Klukowska, Iterative data refinement for soft X-ray microscopyi, Columbia University Medical Center, New York, NY, August 2, 2013. Slides.
Joanna Klukowska, Correcting Blurring in Soft X-ray Microscopy Data To Improve the Reconstructions , The New York Women in Mathematics and Computing Workshop, New York, NY, May 10, 2013. Conference website. Poster (~2Mb).
Joanna Klukowska, Gabor T. Herman, Computational Methods for Inverting the Soft X-Ray Transform, SIAM Conference on Imaging Science 2012, Philadelphia, PA, May 20-22, 2012. Conference website
Younes Benkarroum, Hui Wei, Garrett Katz, Alexandra Alimova, William J. Rice, Al Katz, Doris Bucher, Joanna Klukowska, Gabor T. Herman, Paul Gottlieb, Influenza B Structure Analyzed by Cryo-Electron Microscopy, poster session of 2011 Structural Biology Faculty Retreat, Graduate Center of the City University of New York, June 6, 2011.
Distance-Dependent Blur Correction in 3D Electron and Soft X-ray Microscopy, Minisymposium on Computational Methods for Three-Dimensional Microscopy Reconstruction, Graduate Center of the City University of New York, November 8, 2010. slides
Joanna Klukowska, Gabor T.Herman, Ivan G.Kazantsev, Correction of Distance-Dependent Blurring in Projection Data for Fully Three-Dimensional Electron Microscopic Reconstruction, ISBI 2010. Conference Website, IEEE Xplore.
Finding Mobile Data: Efficiency vs. Location Inaccuracy, ESA 2007, Eilat, Israel, October 8-10, 2007
Other Presentations and Invited Talks
Joanna Klukowska, Inverting the Soft X-Ray Transform, Minisymposium on Computational Methods for Three-Dimensional Microscopy Reconstruction, CUNY Graduate Center, New York, NY, June 15, 2012. Workshop website
Joanna Klukowska, Distance-Dependent Blurring in Bio-Medical Imaging, The 1st GC Interdisciplinary Science Student Conference, New York, NY, April 20, 2012. Conference website. Poster (~7Mb).
We Focus on Distance, Minisymposium on Computational Methods in EM-Related Three Dimensional Reconstruction, Columbia University Medical Center, New York, New York, November 30, 2009. slides
Fully Three-Dimensional Defocus-Gradient Corrected Backprojection in Cryoelectron Microscopy, Workshop on Computational Approaches to Three-Dimensional Electron Microscopy, CUNY Graduate Center, New York, New York, August 1, 2008