VICE DEAN FOR BASIC SCIENCES (VDBS) WORKSHOPS
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🛈 Please note: Certain image, microscopy, and interactive file formats cannot be hosted on this website. These materials will be provided separately during the workshop.
AI Workshop Series
Working with AI: Basic Image Analysis using Large Language Models (LLMs)
Fridays, July 10, 17, 24, and 31, 2026 | 10–11 a.m. | Hybrid
The Foundation: The Language of Seeing
Session 1 • Friday, July 10, 2026
In this first session, Fernando Santana, Ph.D., introduces the foundational concepts for using large language models in scientific image analysis, including how to describe images in four dimensions (sample, imaging, structure, and question), evaluate image quality, and distinguish execution from discovery workflows. Participants learn how to build AI-assisted image analyses, interpret overlays, set thresholds, and validate results against known ground truth before trusting AI-generated results.
Instructor: L. Fernando Santana, Ph.D.
Materials
Data and Files
Calcium Signals
Session 2 • Friday, July 17, 2026
In this session, Fernando Santana, Ph.D., extends AI-assisted image analysis to time-varying calcium imaging. Participants learn how to describe calcium recordings, build and validate a calcium event detector using a large language model, measure calcium sparks, transients, and propagating waves, and use quantitative measurements to generate new biological hypotheses.
Instructor: L. Fernando Santana, Ph.D.
Materials
Data and Files
- Session 2 Practice Dataset - Image and Metadata. (Provided during the workshop)
- Download Session 2 Ground-Truth Reference (CSV)
Segmentation and Colocalization
Session 3 • Friday, July 24, 2026
In this session, Fernando Santana, Ph.D., demonstrates how to build an AI-assisted segmentation and colocalization analysis pipeline for multichannel microscopy images. Participants learn how to segment biological structures, compare multiple colocalization metrics, distinguish meaningful spatial relationships from chance using statistical controls, and validate AI-generated analyses before applying them to their own datasets.
Instructor: L. Fernando Santana, Ph.D.
Materials
Data and Files
- Session 3 Practice Dataset - Image and Metadata. (Provided during the workshop)
Super-Resolution Analysis
Session 4 • Friday, July 31, 2026
In this final session, Manuel F. Navedo-Morales, Ph.D., introduces AI-assisted analysis of super-resolution microscopy data, emphasizing the transition from pixel-based images to localization point clouds. Participants learn how to use large language models to perform cluster analysis, quantify nanoscale spatial organization, validate findings using randomized controls, and build reproducible workflows for single-molecule localization microscopy (SMLM) analysis.
Instructor: Manuel F. Navedo-Morales, Ph.D.
Materials
Data and Files
Q&A |
Coming Soon |
| Questions and answers from all four sessions, organized by topic. | Available after the workshop series. |
Questions or Requests?
For questions about the workshop, assistance with materials, or requests for files that cannot be hosted on this website, please contact:
Adriane Joo, Ph.D. (she/her/hers)
Director of Research Strategy and Innovation for Basic Sciences
HHMI Application Strategy Workshop
Date: Wednesday, July 22, 2026, 1–2 p.m. Pacific Time
Format: Zoom Webinar
Audience: Faculty considering or planning to submit HHMI applications
The HHMI Application Strategy Workshop brought together UC Davis HHMI investigators, Freeman Hrabowski Scholars, and research development leaders to share practical advice on an application process that differs fundamentally from NIH R01 grant writing. Because HHMI invests in scientists rather than individual projects, applicants must convey a bold, cohesive scientific vision, a distinctive research identity, and the potential to pursue high-risk, high-impact questions—not a fixed experimental roadmap. Drawing on their own experiences, panelists discussed how they framed their applications, moved beyond familiar NIH conventions, and positioned their work for HHMI review.
- Bold scientific vision versus detailed experimental roadmap
- Scientific identity, beyond the next set of experiments
- Intellectual ambition and risk-taking in HHMI applications
- Tailoring your narrative to the specific program
- Common pitfalls when transitioning from NIH to HHMI writing
Panelists
- Neil Hunter, Ph.D., HHMI Investigator; Professor, Department of Microbiology and Molecular Genetics, UC Davis
- Siobhan M. Brady, Ph.D., HHMI Investigator; Professor, Department of Plant Biology, UC Davis
- Elisa Zhang, Ph.D., HHMI Freeman Hrabowski Scholar; Assistant Professor, Department of Physiology and Membrane Biology and Department of Obstetrics and Gynecology, UC Davis School of Medicine
- Theanne Griffith, Ph.D., HHMI Freeman Hrabowski Scholar; Associate Professor, Department of Physiology and Membrane Biology, UC Davis School of Medicine
- Erica Chédin, Ph.D., Director, SOM Grants Facilitation
- Matt Boitano, Director, Foundation Engagement
Facilitated by Adriane Joo, Ph.D., Director of Research Strategy and Innovation for Basic Sciences, Dean’s Office, School of Medicine, UC Davis Health.
Workshop Materials
Full Transcript
A cleaned, lightly edited transcript of the full panel discussion and Q&A.
Summarized Q&A
Key takeaways from the discussion, organized by topic.
Application Support and Competition Dates
Faculty planning to apply to the current HHMI competition may contact Matt Boitano, Director of Foundation Engagement, at mboitano@ucdavis.edu for one-on-one support with defining the scope of an application, reviewing draft materials, and receiving detailed feedback.
2028 competition dates:
- Freeman Hrabowski Scholars Program: Applications open Tuesday, Nov. 3, 2026, at 9 a.m. ET and close Tuesday, Dec. 15, 2026, at 11:59 p.m. ET.
- Hanna H. Gray Fellows Program: Applications open Tuesday, Nov. 3, 2026, at 9 a.m. ET and close Tuesday, Dec. 15, 2026, at 11:59 p.m. ET.
Beginning with the 2028 cycle, HHMI will select applicants for these programs through a single, combined competition, with review tailored to each career stage.
HHMI Virtual Event Recording
Hear directly from HHMI’s Science Programs team about its early career programs, what reviewers look for in candidates, and how to prepare a strong application.