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Daniela Ushizima

Daniela (Dani) Ushizima
Staff Scientist / Data Scientist
1 Cyclotron
Mail Stop 59 - office 3017
Berkeley, CA 94720 US

Daniela Ushizima is a Staff Scientist at LBNL and a Data Scientist at the Berkeley Institute for Data Science (BIDS) at UC Berkeley. She leads the Image Processing/Machine Vision team for the Center of Advanced Mathematics for Energy Research Applications (CAMERA) at LBNL. 

Ushizima is the recipient of the U.S. Department of Energy Early Career award (2016-2020)Her research aims to aggregate value to scientific images obtained at DOE facilities by exploring advances in computer vision and machine learning to accelerate science discovery in materials sciences. As part of scientific teams, she has tackled images across domains (ImageXD), experiments, algorithms and learning. As an example, she has been developing pyCBIR, a image recommendation software that drives search, matches and sorting using scientific images across science domains.

Recently, she was nominated by peers to 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, such as Software Carpentry and Black Girls Code. Through the cooperation with UC Berkeley, she has designed algorithms with medical doctors and pathologists improve medical imaging understanding; such work led to her nomination to Science without Borders Special Researcher by CNPq/Brazil for her R&D accomplishments in biomedical image analysis.  [More Research Projects]

Selected publications:

  • MacNeil, Ushizima, Panerai, Mansour, Barnard, Parkinson, "Interactive Volumetric Segmentation for Textile Microtomography Data using Wavelets and Non-local means", Journal of Statistical Analysis and Mining, Sep 2019.

  • Araújo, Silva, Resende, Ushizima, Medeiros, Carneiro, Bianchi, "Deep Learning for Cell Image Segmentation and Ranking", Computerized Medical Imaging and Graphics, Mar 2019.

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

  • 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.

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

  • 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.

  • 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

  • Odziomek, Ushizima, Oberbek, Kurzydlowski, Puzyn, "Scanning electron microscopy image representativeness: morphological data on nanoparticles", Journal of Microscopy, 2016.

  • 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]

  • Ushizima, Bianchi, Carneiro. Segmentation of subcellular compartments combining superpixel representation with voronoi diagrams. IEEE International Symposium on Biomedical Imaging (ISBI) - AWARDED 1st place in Code Competition, April 2014.[NEWS]  

  • 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]

  • 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. 

  • 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", Machine Learning, In-Tech, 367-389, 2010.[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]

  • 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.

  • 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, "Scientific Image Analysis with Convolutional Neural Networks, CoDA 2018, Santa Fe, NM, Mar 2018.
    MacNeil, Ushizima, Banard, Panerai, Parkinson, "Statistical Graphical Models and Deep Learning applied to Textile Composite Specimens", CoDA 2018, Santa Fe, NM, Mar 2018.

  • Alegro, Chen, Castruita, Satrawada, Heinsen, Ushizima, Tsun, Grinberg, “Deep learning for billion-pixel digital pathology analysis: application in mapping Tau protein in the human brain”, Deep Learning in Biomedicine. UCSF, San Francisco CA, 2018.

  • Araujo, Silva, Ushizima, Medeiros, "Searchable datasets in Python: images across domains, experiments, algorithms and learning", PyData San Francisco 2016.PDF

  • Ushizima, Terciano, 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.

  • 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.

  • 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, 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.

  • 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.

  • 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. 

  • 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]

  • 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, 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-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.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 @ Center for Advanced Mathematics for Energy Research Applications - CAMERA

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

Dani @ Teaching Computer Science to the Bay Area community