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
PAST EVENTS
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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