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2023 Spatial Biology Workshop

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  • Registration is now open at

  • The workshop will be hybrid (in-person and virtual)

  • It is free for everyone to attend!



Monday, August 28, 2023

Location: LKSC Berg Hall

7:30am - 8:00am

8:00am - 8:20am

8:20am - 9:20am





9:20am - 9:45am

9:45am - 11:15am










11:15am - 12:00pm

12:00pm - 1:00pm

1:00pm - 2:00pm


Check-in and Registration


  • Mike Angelo (Stanford University)

Cell Detection and Classification

  • Noah Greenwald (Mike Angelo lab, Stanford University)

Segmentation of multiplexed imaging data

  • Candace Liu (Mike Angelo lab, Stanford University)

Robust phenotyping of highly multiplexed tissue imaging data using pixel-level clustering


Cell Detection and Classification

  • Lorenz Rumberger (Kainmueller Lab, Max Delbrück Center for Molecular Medicine, Charité University Hospital)

Nimbus: Improving cell phenotyping by factoring in sub-cellular marker expression patterns

  • Yuval Bussi (Leeat Keren lab, Weizmann Institute of Science)

CellTune: A human-in-the-loop framework for efficient and accurate cell classification in multiplexed images

  • David Van Valen (Caltech)

Everything as code

Role of pathologists in tissue studies

  • Albert Tsai (Stanford University)

Concepts in histology and histopathologic diagnosis for researchers


Workshop: H&E bootcamp

  • Albert Tsai (Stanford University)

Happy Hour at the Rose & Crown

Tuesday, August 29, 2023

Location: LKSC Berg Hall

8:00am - 10:15am





10:15am - 10:40am

10:40am - 12:00pm

12:00pm - 1:00pm

1:00pm - 2:00pm

Applications of Spatial Biology I

  • Denise Kirschner (University of Michigan)

The use of multi-scale computational modeling in spatial biology

  • Nils Gehlenborg (Harvard Medical School)

Vitessce: A framework for visual exploration of spatial single-cell data

  • Russ Butler (AdventHealth University)

The role of micro-GIS in spatial biology

  • Sizun Jiang (Harvard Medical School)

Spatial-omics to interrogate host-disease interactions

  • Luca Marconato (Oliver Stegle lab, European Molecular Biology Laboratory)

SpatialData, an open and universal framework for processing spatial omics data


De Novo Mass Spectrometry

  • Jeff Spraggins (Vanderbilt University)

Constructing integrated multimodal molecular atlases of the human kidney

  • Peggi Angel (Medical University of South Carolina)

Decoding the matrix

  • Richard Drake (Medical University of South Carolina)

Deciphering the glycan code of the tumor tissue microenvironment

  • Ke Leow (Mike Angelo lab, Stanford University)

Multimodal MALDI imaging reveals pro-invasive N-glycans in placenta trophoblasts



  • Erin Diel (Head of Product, Glencoe Software)

Managing and analyzing spatial data with OMERO Plus

Wednesday, August 30, 2023

Location: LKSC Berg Hall

8:00am - 9:20am



9:20am - 9:45am

9:45am - 12:00pm



The Scientific Spectrum of Spatial Analysis

  • Lauren Gillespie (Stanford University, Carnegie Institution for Science)

Mapping plant communities across space and time using deep learning, citizen science, and remote sensing

  • Sean Gasiorowski (SLAC National Accelerator Laboratory)

Neural fields and differentiable simulation for spatial analysis in atomic and particle physics

  • Akshay Chaudhari (Stanford University)

Data efficient deep learning methods in radiology


Applications of Spatial Biology II

  • Barbara Engelhardt (Stanford University, Gladstone Institutes)

Designing experiments for atlas building

  • Emma Lundberg (Stanford University)

Spatial proteome biology from subcellular to tissue level

  • John Hickey (Duke University)

Spatial frameworks and tools for mapping the human intestine

  • Joakim Lundeberg (SciLifeLab, KTH Royal Institute of Technology)

Spatial multiomics in a single tissue section

  • Inna Averbukh (Mike Angelo lab, Stanford University)

A spatially resolved timeline of the human maternal–fetal interface




  • The workshop will be held at Stanford School of Medicine, Li Ka Shing Learning and Knowledge Center (LKSC), Berg Hall:

  • SFO and SJC are the closest airports.

  • Lodging options close to campus:​​

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