BIDS ImageXD 2021

Image Analysis Across Domains

XD

May 17, 2021 to May 18, 2021
10:00am to 2:00pm
Virtual Participation

Cost

$0

Register

BIDS ImageXD banner logoBIDS ImageXD 2021

Image Analysis Across Domains 
Dates: May 17-18, 2021 (Monday and Tuesday)
Time: 10:00 AM – 2:00 PM Pacific (each day)
Register for ImageXD 2021

BIDS ImageXD convenes researchers, scientists, and theorists (of all learning levels) who work with images as a primary source of data, to learn about the latest developments in a variety of fields and to promote interdisciplinary collaboration. This year’s event will feature a 2-day program of distinguished speakers and presentations. All researchers, scientists, and theorists who work with images as a primary source of data are welcome and encouraged to attend this event. To receive upcoming announcements, sign up for the BIDS Mailing List

Program Summary (View the Full Program)
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Day 1: MONDAY, May 17

10:00 – 11:00 AM — Session 1: Global Change

Novel indicators of biodiversity contributions on ecosystem stability from multi-temporal remote sensing data • Iryna Dronova, Associate Professor, Department of Environmental Science, Policy & Management, Rausser College of Natural Resources, and Department of Landscape Architecture & Environmental Planning, College of Environmental Design, UC Berkeley   
Hydrologic Applications of Data Assimilation • Manuela Girotto, Assistant Professor, Department of Environmental Science, Policy & Management, Rausser College of Natural Resources, UC Berkeley 
Presentation/Speaker TBA

11:00 AM – 12:00 PM — Session 2: Environmental and Social Justice 

◦ Lakóta GeoSpatial Applications of the Black Hills Area - Makówapi Wítaya (Geography Together) • James J. Sanovia, Faculty - GIS Lab Manager, STEM Department, Oglala Lakota College 
◦ Presentation TBA • Sam Gregory, Program Director, WITNESS
◦ Presentation/Speaker TBA

12:00 – 1:00 PM — Session 3: Tools & Methods I 

◦ PyTorch3D • Jeremy ReizensteinFacebook AI Research, London 
◦ 3D building reconstruction and analysis from RGB drone imagery • Avideh Zakhor, Chair & Professor, Electrical Engineering and Computer Science, UC Berkeley
◦ Superpixels, Supervoxels, and Adaptels • Sabine Süsstrunk, Professor, Ecole Polytechnique Fédérale de Lausanne (EPFL)

1:00 – 2:00 PM — ImageXD Community 

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Day 2: TUESDAY, May 18

10:00 – 11:00 AM — Session 4: Materials Science

◦ GPU-accelerated Data Science with RAPIDS • Zahra Ronaghi, System Software Manager, NVIDIA
◦ Space-Time Correspondence as a Contrastive Random Walk • Allan Jabri, PhD student, EECS, UC Berkeley
◦ Quantifying solidification of metallic alloys with scikit-image • Marianne Corvellec, scientific software developer, scikit-image core team and independent researcher, Institute for Globally Distributed Open Research and Education (IGDORE); and C. Gus Becker, PhD student, Center for Advanced Non-Ferrous Structural Alloys (CANFSA)

11:00 AM – 12:00 PM — Session 5: Health

◦ High throughput lesion evaluation and quality control for incorporating quantitative imaging metrics into clinical practice • Anisha Keshavan, Lead Data Scientist, Octave Bioscience 
◦ Pathology Image Analysis with Deep Learning • Saeed Hassanpour, Associate Professor of Biomedical Data Science, Computer Science, and Epidemiology; Geisel School of Medicine at Dartmouth
◦ Computational Image Phenotyping for Stroke and Prostate Cancer • Corey Arnold, Associate Professor, UCLA Departments of Radiology, Pathology, Bioengineering, and Electrical & Computer Engineering

12:00 – 1:00 PM — Session 6: Tools & Methods II 

◦ The ImageJ Ecosystem • Kevin Eliceiri, Professor of Medical Physics and Biomedical Engineering, Morgridge Institute for Research and University of Wisconsin-Madison
◦ napari: a fast, interactive, multi-dimensional image viewer for python • Nick Sofroniew, Imaging Product Lead, Chan Zuckerberg Initiative
◦ Automated quantification and analysis of human brain connections • Ariel Rokem, Research Assistant Professor, Department of Psychology and eScience Institute, University of Washington

1:00 – 2:00 PM — ImageXD Community 

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Program Committee

  • Laura Waller, Chair, Associate Professor, Electrical Engineering and Computer Sciences, UC Berkeley
  • Alvin Cheung, Assistant Professor, EECS, UC Berkeley
  • Maggi Kelly, Professor of Environmental Science, Policy,and Management and Faculty Director of the Geospatial Innovation Facility, UC Berkeley
  • David Mongeau, BIDS Executive Director, UC Berkeley
  • Daniela Ushizima, Staff Scientist, Computational Research Division, LBNL
  • Maryam Vareth, BIDS Health and Life Sciences Lead and Co-Director, Innovate For Health initiative, UC Berkeley and UCSF

Organizing Commitee

  • Adam Anderson, BIDS Research Training Program Manager
  • Alexandre de Siqueira, BIDS Researcher
  • Marsha Fenner, BIDS Communications/Program Manager

BIDS ImageXD (Images Across Domains) is a cross-domain initiative that promotes interdisciplinary collaboration and training for researchers, scientists, and theorists in a variety of fields across STEAM who work with images as a primary source of data, and who collaborate together to identify common principles, algorithms, and tools to build computational platforms and solve image analyses problems across disciplinary boundaries.

Speaker(s)

Laura Waller

Associate Professor, Electrical Engineering and Computer Sciences, UC Berkeley

Laura Waller works on computational imaging and microscopy methods for biological, industrial, and commercial applications. She is an associate professor at UC Berkeley in the Department of Electrical Engineering and Computer Sciences (EECS), with affiliations in Bioengineering, QB3, and Applied Sciences & Technology. She was a postdoctoral researcher and lecturer of physics at Princeton University from 2010 to 2012 and received BS, MEng, and PhD degrees from the Massachusetts Institute of Technology in 2004, 2005, and 2010, respectively. She is a Moore Foundation Data-Driven Investigator, Bakar fellow, NSF CAREER awardee, and Packard fellow.

Alvin Cheung

Assistant Professor, EECS, UC Berkeley

Alvin Cheung is an assistant professor of Electrical Engineering and Computer Science at UC Berkeley. His research interests include all aspects of data management and programming systems. He is also interested in helping non-technical users write code by developing new programming languages, user interfaces, and different modalities. Before joining Berkeley, he was on the faculty at the University of Washington’s school of computer science & engineering, where he was also an faculty affiliate at the eScience Institute. Alvin's research has been recognized through multiple early career awards such as the US Presidential Early Career Award for Scientists and Engineers, the Sloan Fellowship, along with a number of best paper and demo awards.

Alexandre de Siqueira

Postdoctoral Researcher

Alex is a postdoctoral researcher at BIDS, working on open source algorithms for processing computed tomography (CT) 3D images. He received his MS and PhD from the State University of São Paulo, Brazil, applying image processing tools to tackle challenges in materials science and geochronology. A core developer of scikit-image, he is an open source and free software enthusiast since his first contact with Linux, in 2000, contributing to several projects and events in Latin America and Europe. Alex also worked as a postdoctoral fellow at the State University of Campinas, Brazil, and the TU Bergakademie Freiberg, Germany, where he created pytracks and wrote Octave - Your first steps on scientific programming (in Brazilian Portuguese).

Marsha Fenner

Communications/Program Manager, Berkeley Institute for Data Science

Marsha Fenner works to connect researchers, facilitate interdisciplinary collaboration and implement training, education, and outreach programs that enhance and expand BIDS' and Berkeley’s vibrant and diverse data science community.  She focuses on developing new programs and events that engage the entire data science community by strengthening partnerships and integrating research efforts among a wide array of disciplines and departments across campus and beyond.  Marsha has managed communications, training/education/outreach programs and administrative operations for scientific programs and research initiatives at UC Berkeley and Lawrence Berkeley National Laboratory, including the Innovative Genomics Institute, the DOE Joint Genome Institute and the LBL Advanced Light Source.  She holds an MA in philosophy and comparative religious studies, and a BA in classics, philosophy and mathematics.

Maggi Kelly

Professor; Environmental Science, Policy,and Management; UC Berkeley

BIDS Senior Fellow Maggi Kelly is Professor and Cooperative Extension Specialist in the Environmental Science, Policy and Management department at UC Berkeley. Her group uses a range of geospatial data and analytics – from spatial modeling, remote sensing, drones, liDAR, historical archives, surveys, participatory mapping, and the field - to gain insights about how and why California landscapes are changing, and what that change means for those who live on, use, and manage our lands. Her work enables interdisciplinary collaboration, data-rich analytics research, and active outreach across a number of scientific domains (forests, agriculture, wetlands, climate change) with significant societal impact. She is faculty director of the Geospatial Innovation Facility and Director of the ANR Statewide Program in Informatics and Geographic Information Systems (IGIS).

David Mongeau

Executive Director

David Mongeau is the Executive Director of BIDS.  With the Director and Faculty Council, he sets strategic direction and oversees the institute’s research, training, and outreach.  David also leads the institute’s industry and foundation relations and its engagement with other UC and global research institutes – all toward the overarching mission at BIDS to create and deploy data science methods, practices, and technologies to enable discovery. 

Previously, David co-led the data analytics institute at Ohio State; worked at Battelle, where he championed its proposal for an AI and cybersecurity company, now Covail; and worked for many years at Bell Labs – starting on the team that introduced the first C++ compiler and UNIX System V and leaving after building a global business and technology consulting practice, now part of Nokia Bell Labs Consulting.

David earned his undergraduate degree at Carnegie Mellon University, and later earned a graduate degree at Rensselaer Polytechnic Institute and an MBA from Purdue University. Many of his interests lie beyond data science, embracing the humanities and arts.

Daniela Ushizima

Staff Scientist, Computational Research Division, LBNL

BIDS Faculty Affiliate Dani Ushizima is a Staff Scientist in the Computational Research Division at LBNL, where she leads the Image Processing/Machine Vision team at CAMERA. She also leads the Center for Recognition and Inspection of Cells (CRIC), where her research focuses on imaging cancer cells for early-stage disease diagnosis. With 20 years of research and development experience in Computer Vision, Dani has focused primarily on quantitative microscopy and microstructure classification, from materials science to biomedical imaging.

Maryam Vareth

Health and Life Sciences Lead

Maryam Vareth leads BIDS’ data science research efforts in the Health & Life Sciences.  Dr. Vareth is a Co-Director of the Innovate For Health initiative, a collaboration among UC Berkeley, UCSF, and Janssen Pharmaceutical Companies of Johnson & Johnson. As an experienced engineer, researcher, and data scientist, she applies mathematics, statistics and physics to solve unmet needs in healthcare to enhance patients’ experience during their medical journey. She is an advocate for “data-driven” medicine, and in particular for linking medical imaging data with medical diagnostics and therapeutics to extract clinically-relevant insights through the use of open research and open source practices.  Dr. Vareth received her BS and MS training in Electrical Engineering and Computer Science (EECS) from UC Berkeley, where she was awarded the prestigious Regent’s and Chancellor’s Scholarship.  She completed her PhD through the joint UC Berkeley-UCSF Bioengineering program as a National Science Foundation Fellow, where she was awarded the Margaret Hart Surbeck Endowed Fellowship for Interdisciplinary Research for her work on developing new techniques and algorithms for the acquisition, reconstruction and quantitative analysis of Magnetic Resonance Spectroscopy Imaging (MRSI), with the goal of improving its speed, sensitivity and specificity to improve the management of patients with brain tumors.  She conducted her post-doctoral fellowship at UCSF, combining structural, physiological and metabolic imaging data from large clinical trials to quantitatively characterize heterogeneity within malignant brain tumors.

Jim Sanovia

Faculty - Researcher, Math and Science, Oglala Lakota College

Sam Gregory

Program Director, WITNESS

Jeremy Reizenstein

PyTorch3D Team, Facebook AI Research, London

Avideh Zakhor

Chair & Professor, Electrical Engineering and Computer Science, UC Berkeley

Sabine Süsstrunk

Professor and Director of the Images and Visual Representation Laboratory in the School of Computer and Communication Sciences, EPFL

Zahra Ronaghi

System Software Manager, NVIDIA

Allan Jabri

PhD student, EECS, UC Berkeley

Marianne Corvellec

scikit-image

C. Gus Becker

PhD student, Center for Advanced Non-Ferrous Structural Alloys (CANFSA)

Anisha Keshavan

Lead Data Scientist, Octave Bioscience

Saeed Hassanpour

Associate Professor of Biomedical Data Science, Computer Science, and Epidemiology; Geisel School of Medicine at Dartmouth

Corey Arnold

Associate Professor, UCLA Departments of Radiology, Pathology, Bioengineering, and Electrical & Computer Engineering

Kevin Eliceiri

Professor of Medical Physics and Biomedical Engineering, Morgridge Institute for Research and University of Wisconsin-Madison

Nick Sofroniew

Imaging Product Lead, CZI Science Technology

Iryna Dronova

Associate Professor of Landscape Architecture & Environmental Planning, Department of Environmental Science, Policy & Management, Rausser College of Natural Resources, UC Berkeley

Ariel Rokem

Assistant Professor, Department of Psychology, University of Washington

Manuela Girotto

Assistant Professor, Department of Environmental Science, Policy & Management, Rausser College of Natural Resources, UC Berkeley