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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, Ph.D. is a Staff Scientist at LBNL, also affiliated with the Berkeley Institute for Data Science (BIDS) at UC Berkeley, and the Bakar Institute at UC San Francisco. She leads the Computer Vision team for the Center of Advanced Mathematics for Energy Research Applications (CAMERA) at LBNL. Ushizima constructs algorithms to extract information from scientific images. Together with her team, they develop computer vision software that exploits advanced machine learning and datasets from microscopes (e.g. X-ray, electron, tomography) for decision-making. Research also includes machine learning applied to text mining and natural language processing. She has led projects ranging from quality control of materials to biomedical image analysis. Awarded DOE Early Career fellowship in 2016. Development of pyCBIR, an image recommendation software. Nominated the LBNL Director's Award in 2017, followed by the LBNL [email protected] in 2018, and the Latina Scientist in 2021. Scientific diplomacy with the U.S. Dept. of State TechWomen. Cooperation with UC San Francisco in the design of algorithms to improve cell counting and analyses of biomedical imaging. (Visit the IDEAL project website for more.)

Selected publications:

  • Sadre, Majumdar, Sundaram, Ushizima, "Validating deep learning inference during chest X-ray classification for COVID-19 screening", Nature Scientific Reports 2021.
  • Rezende, Silva, Bernardo, Tobias, Oliveira, Machado, Costa, Medeiros, Ushizima, Carneiro, Bianchi, "Cric searchable image database as a public platform for conventional pap smear cytology data”, Nature Scientific Data 2021, 10.1038/s41597-021-00933-8.
  • Noack, Zwart, Ushizima, Fukuto, Yager, Elbert, Murray, Stein, Doerk, Tsai, Li, Freychet, Zhernenkov, Holman, Lee, Chen, Rotenberg, Weber, Le Goc, Boehm, Steffens, Mutti, Sethian, "Gaussian Processes for Autonomous Data Acquisition at Large-Scale X-Ray and Neutron Scattering Facilities", Nature Reviews Physics, 2021 [pdf]. 
  • Miramontes, Piergies, Grinberg, Ushizima, "Accelerating Quantitative Microscopy with U-Net-based Cell Counting", IEEE XVIII International Symposium on Biomedical Imaging (ISBI) Apr 2021.
  • Panod, Ercius, Monteiro, Scott, Ushizima, Li, Xu, Wenk, "3D Nanotomography of Calcium Silicate Hydrates by Transmission Electron Microscopy", Journal of the American Ceramic Society 2020.
  • 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.
  • 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]
  • 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.

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