THE ANGELO LAB
Stanford University
2023 Spatial Biology Workshop
Agenda
Playlist of all recorded talks here
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
5:00pm
Check-in and Registration
Introduction
-
Mike Angelo (Stanford University) [video]
Cell Detection and Classification
-
Noah Greenwald (Mike Angelo lab, Stanford University) [video]
Segmentation of multiplexed imaging data
-
Candace Liu (Mike Angelo lab, Stanford University) [video]
Robust phenotyping of highly multiplexed tissue imaging data using pixel-level clustering
Break
Cell Detection and Classification
-
Lorenz Rumberger (Kainmueller Lab, Max Delbrück Center for Molecular Medicine, Charité University Hospital) [video]
Nimbus: Improving cell phenotyping by factoring in sub-cellular marker expression patterns
-
Yuval Bussi (Leeat Keren lab, Weizmann Institute of Science) [video]
CellTune: A human-in-the-loop framework for efficient and accurate cell classification in multiplexed images
-
David Van Valen (Caltech) [video]
Everything as code
Role of pathologists in tissue studies
-
Albert Tsai (Stanford University) [video]
Concepts in histology and histopathologic diagnosis for researchers
Lunch
Workshop: H&E bootcamp
-
Albert Tsai (Stanford University) [video]
Happy Hour at the Rose & Crown
-
547 Emerson St, Palo Alto
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) [video]
The use of multi-scale computational modeling in spatial biology
-
Nils Gehlenborg (Harvard Medical School) [video]
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) [video]
SpatialData, an open and universal framework for processing spatial omics data
Break
De Novo Mass Spectrometry
-
Jeff Spraggins (Vanderbilt University) [video]
Constructing integrated multimodal molecular atlases of the human kidney
-
Peggi Angel (Medical University of South Carolina) [video]
Decoding the matrix
-
Richard Drake (Medical University of South Carolina) [video]
Deciphering the glycan code of the tumor tissue microenvironment
-
Ke Leow (Mike Angelo lab, Stanford University) [video]
Multimodal MALDI imaging reveals pro-invasive N-glycans in placenta trophoblasts
Lunch
Seminar
-
Erin Diel (Head of Product, Glencoe Software) [video]
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
12:00pm
The Scientific Spectrum of Spatial Analysis
-
Lauren Gillespie (Stanford University, Carnegie Institution for Science) [video]
Mapping plant communities across space and time using deep learning, citizen science, and remote sensing
-
Sean Gasiorowski (SLAC National Accelerator Laboratory) [video]
Neural fields and differentiable simulation for spatial analysis in atomic and particle physics
-
Akshay Chaudhari (Stanford University) [video]
Data efficient deep learning methods in radiology
Break
Applications of Spatial Biology II
-
Barbara Engelhardt (Stanford University, Gladstone Institutes) [video]
Designing experiments for atlas building
-
Emma Lundberg (Stanford University) [video]
Spatial proteome biology from subcellular to tissue level
-
John Hickey (Duke University) [video]
Spatial frameworks and tools for mapping the human intestine
-
Joakim Lundeberg (SciLifeLab, KTH Royal Institute of Technology) [video]
Spatial multiomics in a single tissue section
-
Inna Averbukh (Mike Angelo lab, Stanford University) [video]
A spatially resolved timeline of the human maternal–fetal interface
Conclusion