Daniela Ushizima

Dani Ushizima, Ph.D., is a Staff Scientist at Berkeley Lab, also Affiliated Faculty with the Berkeley Institute for Data Science (BIDS) at UC Berkeley, and the Bakar Institute at UC San Francisco. She leads the Machine Learning (ML) team for the Center of Advanced Mathematics for Energy Research Applications (CAMERA) at LBNL. Ushizima has constructed algorithms to extract information from scientific data. Together with her team, they develop computer vision software that exploits advanced ML and datasets from microscopes (e.g. X-ray, electron, tomography) for decision-making. Research also includes ML such as transformers applied to 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 Women@Lab in 2018, the Latina Scientist in 2021 and the PMWC Pioneer Award in 2023. 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 Ushizima's website for more information.

Selected publications:

• Huang, Perlmutter, Su, Quenum, Shevchenko, Parkinson, Zenyuk, Ushizima, “Detecting lithium plating dynamics in a solid-state battery with operando X-ray computed tomography using machine learning”. Nature Computational Materials 2023 [link]
• Ushizima, Chen, Alegro, Ovando, Eser, Lee, Poon, Shankar, Kantamneni, Satrawada, Amaro Jr, Heinsen, Tosun, Grinberg, "Deep learning for Alzheimer's disease: Mapping large-scale histological tau protein for neuroimaging biomarker validation", NeuroImage 2022 [link]
• Siqueira, Ushizima, van der Walt, “A reusable pipeline for large-scale fiber segmentation on unidirectional fiber beds using fully convolutional neural networks”, Nature Scientific Data 2022 [pdf]
• 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 detection on SAR images using level set methods, IEEE Transactions on Systems, Man and Cybernetics Part C (39):2:214-222.
• 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 Staff Scientist @ Center for Advanced Mathematics for Energy Research Applications - CAMERA

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

Dani Affiliate Faculty @ Bakar Institute - University of California, San Francisco

Dani Volunteer @ Teaching computer science skills in the Bay Area community