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Daniela Ushizima

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Daniela (Dani) Ushizima
Staff Scientist / Deputy Group Lead / BIDS Data Scientist Fellow
Phone: +1 510 486 4061
1 Cyclotron
Mail Stop 50F 1650 - office 1614
Berkeley, CA 94720 US

Daniela Ushizima is a Staff Scientist at LBNL and a Data Scientist at BIDS. Her research aims to aggregate value to scientific data by constructing models, algorithms and software that explore advanced machine learning, e.g. convnets, and leverage unlabeled massive datasets and minimal curations by domain scientists. Ushizima leads the Image Processing/Machine Vision team for the Center of Advanced Mathematics for Energy Research Applications (CAMERA) at LBNL. She has been in charge of projects with applications ranging from biomedical image analysis to quality control in the design of new materials. Ushizima is the recipient of the U.S. Department of Energy Early Career award (2016-2020), the LBNL Director's Award (2017), and LBNL Women@Lab (2018)  for her work on data science and machine learning, as well as activities on scientific diplomacy with the U.S. Dept. of State TechWomen and other educational efforts. As a Science without Borders Special Researcher awardee (CNPq/Brazil), her R&D activities focuses on “smart cytology” for women's healthcare, and building the next generation workforce.

[More info about research projects]

[Science to the community]

Selected publications:

  • Ke, Brewster, Yu, Yang, Ushizima, Sauter, "A Convolutional Neural Network-Based Screening Tool for X-ray Serial Crystallography", Journal of Synchrotron Radiation 2018 (accepted).

  • Araujo, Silva, Ushizima, Parkinson, Hexemer, Carneiro, Medeiros, "Reverse Image Search for Scientific Data within and beyond the Visible Spectrum", Expert Systems and Applications 2018 (accepted).

  • Pandolfi, Allan, Arenholz, Barroso-Luque, Campbell, Caswell, Blair, Carlo, Fackler, Fournier, Freychet, Fukuto, Gursoy, Jiang, Krishnan, Kumar, Kline, Li, Liman, Marchesini, Mehta, N'Diaye, Parkinson, Parks, Pellouchoud, Perciano, Ren, Sahoo, Strzalka, Sunday, Tassone, Ushizima, Venkatakrishnan, Yager, Zwart, Sethian, Hexemer, Xi-cam: A versatile interface for data visualization and analysis, Journal of Synchrotron Radiation 2018 (accepted).

  • Araujo, Silva, Medeiros, Farias, Calaes, Bianchi, Ushizima, "Active contours for overlapping cervical cell segmentation", International Journal of Biomedical Engineering and Technology 2018 (accepted).
  • Williams, Ushizima, Zhu, Anders, Milliron, Helms, "Nearest-Neighbour Nanocrystal Bonding Dictates Framework Stability or Collapse in Colloidal Nanocrystal Frameworks", Chemical Communications, Royal Society of Chemistry, 2017.[PDF]
    Alegro, Theofilas, Nguy, Castruita, Seeley, Ushizima, Grinberg, Automating Cell Detection and Classification in Human Brain Fluorescent Microscopy Images Using Dictionary Learning and Sparse Coding, Journal of Neuroscience Methods, 2017.

  • D. Ushizima, Lights, CAMERA, Action: how machine learning is improving your takes, Advanced Light Source User Meeting 2017, Lawrence Berkeley National Laboratory, Oct 2017. [PDF]
  • D. Ushizima, H. A. Bale, W. Bethel, P. Ercius, B. Helms, H. Krishnam, L. Grinberg, M. Haranczyk, M. A. A. Macdowell, K. Odziomek, D. Y. Parkinson, T. Perciano, R. Ritchie, and C. Yang. IDEAL: Images across Domains, Experiments, Algorithms and Learning, Journal of Minerals, Metals and Materials, 2016. JOM, 68(11), 2963-2972. doi:10.1007/s11837-016-2098-4 - Report Number: LBNL-1006616 [BibTeX]
  • Odziomek, Ushizima, Oberbek, Kurzydlowski, Puzyn, "Scanning electron microscopy image representativeness: morphological data on nanoparticles", Journal of Microscopy, 2016.[PDF]
  • Santos, Bianchi, Ushizima, Pavinatto, Bianchi, "Ammonia gas sensor based on the frequency-dependent impedance characteristics of ultrathin polyaniline films", Sensors and Actuators A: Physical, 2016.[PDF]
  • Lu, Carneiro, Bradley, Ushizima, Nosrati, Bianchi, Carneiro, Hamarneh, "Evaluation of Three Algorithms for the Segmentation of Overlapping Cervical Cells", IEEE Journal of Biomedical and Health Informatics, 99, pp. 2168-2194, 2016.[PDF]
  • Araujo, Silva, Ushizima, Medeiros, "Searchable datasets in Python: images across domains, experiments, algorithms and learning", PyData San Francisco 2016.[PDF]
  • D.M. Ushizima, T. Perciano, H. Krishnan, B. Loring, H. Bale, D. Parkinson, and J. Sethian. Structure recognition from high resolution images of ceramic composites. IEEE International Conference on Big Data, October 2014.
  • D.M. Ushizima, A.G.C. Bianchi, and C. Carneiro. Segmentation of subcellular compartments combining superpixel representation with voronoi diagrams. IEEE International Symposium on Biomedical Imaging (ISBI) - 1st place in Code Competition, April 2014.[pdf]  [NEWS]  [VIDEO]
  • Ushizima, D.M., Bianchi, A.G.C., Krishnam, H., "Challenges and New Developments in Imaging with Large Data Sets", Joint Statistical Meeting (JSM2013), Montreal, Aug 2013.
  • Paula Jr., I.C., Medeiros, F.N.S, Bezerra, F.N. and Ushizima, D.M., "Multiscale Corner Detection in Planar Shape", Journal of Mathematical Imaging and Vision, July 2012.[pdf]
  • Ushizima, D.M., Morozov, D, Weber, G.H., Bianchi, A.G.C. and Bethel E.W., "Augmented topological descriptors of pore network", in: IEEE Trans. Comp Graph. and Vis. USA. 2012.[pdf] [DETAILS ABOUT THE PROJECT]
  • E.A. Carvalho, D.M. Ushizima, F.N.S. Medeiros, C.I.O. Martins, R.C.P. Marques, I.N.S. Oliveira, "SAR imagery segmentation by statistical region growing and hierarchical merging", Digital Signal Processing, Elsevier, Volume 20, Issue 5, Pages 1365-1378, Sept 2010.#20 Top Hottest Paper by ScienceDirect [bib]
  • Ushizima, D.M., Geddes, C.G.R., Cormier-Michel, E., Bethel, E.W., Jacobsen,J., Prabhat, Ruebel, O., Weber, O., Hamann, B., Haggen, H., "Automated Detection and Analysis of Particle Beams in Laser-plasma Accelerator Simulations", In-Tech, 367-389, 2010.[bib][pdf]
  • Leite, G.C., Ushizima, D.M., Medeiros, F.N.S., de Lima, G.G., "Wavelet Analysis for Wind Fields Estimation", Sensors, MDPI Press, ISSN 1424-8220, 10(6):5994-6016, 2010.[pdf][bib]
  • Marques R C P, Medeiros F N S, Ushizima D M (2009), Target dectection on SAR images using level set methods, IEEE Transactions on Systems, Man and Cybernetics Part C (39):2:214-222. [pdf]
  • O. Rubel, C.G.R. Geddes, E. Cormier-Michel, K. Wu, Prabhat, G.H. Weber, D.M. Ushizima, P. Messmer, H. Hagen, B. Hamann, and E.W. Bethel, "Automatic Beam Path Analysis of laser Wakefield Particle Acceleration Data", IOP Computational Science & Discovery, 2 015005 (38pp), Nov, 2009, LBNL-2734E.
  • C. G. R. Geddes, E Cormier-Michel, E. H. Esarey, C. B. Schroeder, J.-L. Vay, W. P. Leemans, D. L.. Bruhwiler, J. R. Cary, B. Cowan, M. Durant, P. Hamill, P. Messmer, P. Mullowney, C. Nieter, K. Paul, S. Shasharina, S. Veitzer, G. Weber, O. Rubel, D. Ushizima, Prabhat, E. W.Bethel, K. Wu. "Large Fields for Smaller Facility Sources." SciDAC Review, Number 13, Summer 2009. LBNL-2299E
  • Ushizima Sabino D M, Costa LF, Calado RT, Zago MA (2004), A texture approach to leukocyte recognition, Real-Time Imaging 10(4):205-216.
  • Ushizima Sabino D M, Costa LF, Zago MA (2003), Automatic leukemia diagnostic, Acta Microscopica (12)1:1-6.

Others publications:

  • Ushizima, D.M., Bianchi, A.G.C., deBianchi, C. and Bethel E.W., "Material science image analysis using quant-CT in ImageJ", in: ImageJ User and Developer Conference 2012, Oct, Luxembourg, LX. [pdf]
  • Ushizima, D.M., Morozov, D, Weber, G.H., Bianchi, A.G.C. and Bethel E.W., "Augmented topological descriptors of pore network", in: VisWeek 2012, Oct, Seattle, WA, USA. [pdf]
  • E. Wes Bethel, David Camp, Hank Childs, Mark Howison, Hari Krishnan, Burlen Loring, Joerg Meyer, Prabhat, Oliver Ruebel, Daniela Ushizima, Gunther Weber. Towards Exascale: High Performance Visualization and Analytics – Project Status Report. Technical Report LBNL-5767E. Lawrence Berkeley National Laboratory, Berkeley CA, USA, 94720. June, 2012. In DOE Exascale Research Conference, April 16–18, 2012, Portland OR, USA. (bibtex) (PDF)
  • Ushizima, D.M., Ajo-Franklin, J., Macdowell, A., Morozov, D., Nico, P., Parkinson, Bethel E.W, Sethian J.A., "Statistical segmentation and porosity quantification of 3D x-ray microtomography", in SPIE Optics and Photonics: XXXIV Applications of Digital Image Processing, Vol.8135-1, pp.1-14, Aug 2011, San Diego, CA, USA. [pdf]
  • Ushizima, D.M., Weber, G.H., Ajo-Franklin, J., Kim, Y., Macdowell, A., Morozov, D., Nico, P., Parkinson, D., Trebotich, D., Wan, J., and Bethel E.W., "Analysis and visualization for multiscale control of geologic CO2", in: Journal of Physics: Conference Series, Proceedings of SciDAC 2011, July 2011, Denver, CO, USA. [pdf]
  • G.Leite, F.Medeiros, D.Ushizima, "Direction Estimation Using Texture Analysis", IEEE XVIII International Conference of Electrical, Electronic and Systems, Aug 8-13 2011.
  • A.Uselton, K.Antypas, D.M.Ushizima, J.Sukharev, "File System Monitoring as a Window Into User I/O Requirements", CUG-2010, Edinburgh, UK, May 24-27th, 2010.
  • D. M. Ushizima, F. N. S. Medeiros, J. Cuadros, C. I. O. Martins, "Vessel Network Detection Using Contour Evolution and Color Components", Proceedings of the 32nd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Buenos Aires, Argentina. Sept 2010.[bib]
  • O.Rubel, S.Ahearn, E.W.Bethel, M.D.Biggin, H.Childs, E.Cormier-Michel, A.DePace, M. Eisen, C.Fowlkes, C.G.R. Geddes, H.Hagen, B.Hamann, M.Huang, S.V.E.Keranen, D.W.Knowles, C.L.Luengo Hendriks, J.Malik, J.Meredith, P.Messmer, Prabhat, D.Ushizima, G.H.Weber and K.Wu, "Coupling visualization and data analysis for knowledge discovery from multi-dimensional scientific data", ICCS'2010, Procedia Computer Science Volume 1, Issue 1, May 2010, Pages 1751-1758. [pdf]
  • C.I.O.Martins, D.M.Ushizima, F.N.S.Medeiros, F.N.Bezerra, R.C.P.Marques, N.D.A.Mascarenhas, "Iterative Self-dual Reconstruction on Radar Image Recovery", Proc. of IEEE Workshop on Applications of Computer Vision, Snowbird, Utah, 37-42, 2009.
  • E. W. Bethel, C. Johnson, S. Ahern, J. Bell, P.-T. Bremer, H. Childs, E. Cormier-Michel, M. Day, E. Deines, T. Fogal, C. Garth, C. G. R. Geddes, H. Hagen, B. Hamann, C. Hansen, J. Jacobsen, K. Joy, J. Kruger, J. Meredith, P. Messmer, G. Ostrouchov, V. Pascucci, K. Potter, Prabhat, D. Pugmire, O. Rubel. Sanderson, C. Silva, D. Ushizima, G. Weber, B. Whitlock, K. Wu. "Occam's Razor and Petascale Visual Data Analysis." In Journal of Physics Conference Series, Proceedings of SciDAC 2009. LBNL-2210E.
  • *Ushizima D M, Rubel O, Prabhat, Weber G, Bethel E W, Aragon C, Geddes C, Cormier-Michel E, Hamann B, Messmer P, Hagen H. "Automated Analysis for Detecting Beams in Laser Wakefield Simulations". 2008 Seventh International Conference on Machine Learning and Applications, Proceedings of IEEE ICMLA'08, 2008. LBNL-960E
  • *Ushizima D M, Calado R T, Rizzatti E G (2006), Leukocyte detection using nucleus contour propagation, Lecture Notes in Computer Science, LNCS 4091: 389-396.
  • Ushizima D M, Lourega L V, Freitas G D, d'Ornellas M C (2006), A Hybrid Image Segmentation Approach using Linear and Non-Linear Processing , International Symposium on Vision by Brains and Machines, Montevideo, Uruguay. CD-Rom.
  • Ushizima D M, Lorena A C, Carvalho A C P L F (2005), Support vector machines applied to white blood cell recognition, V International Conference on Hybrid Intelligent Systems, pp. 379-384.
  • Ushizima D M, Costa L da F, Zago M A (2005), Lymphocytic leukemia under machine vision, XVI Brazilian Symposium on Computer Graphics and Image Processing.
  • *Ushizima-Sabino D M, Costa L da F, Rizzatti E G, Zago M A, (2004), Toward leukocyte recognition using morphometry, texture and color, Proc. of IEEE International Symposium on Biomedical Imaging: From Nano To Macro (ISBI'04), Washington D.C., USA (awarded).
  • Ushizima-Sabino D M, Costa L da F, Rizzatti E G, Zago M A, (2003), A texture approach to leukocyte recognition, Proc. Intern. Conference on Bioinformatics and Computational Biology, Ribeirao Preto, Brazil. CDRom.
  • Ushizima-Sabino, D M., Costa, L.F., Calado, R.T., Zago, M.A. (2002), Chromatin texture characterization using multiscale fractal dimension, IEEE Proc. of 14th International Conference on Digital Signal Processing, Santorini, Greece, (2)1: 529-533.

Dani @ Data Analytics and Visualization - CRD

Dani @ Center for Advanced Mathematics for Energy Research Applications - CAMERA

Dani @ Berkeley Institute of Data Sciences (BIDS) - University of California, Berkeley