Focus Session: Leveraging open-source image-based experimental and computational tools to investigate dynamic stem cell states

Date/Time: Wednesday, 11 June 2025 from 2:00 – 3:30pm (14:00 – 15:30)

Location: Hall B, L1

The Allen Institute for Cell Science aims to understand the ways multicellular systems organize, behave, and transition between cell states. We integrate experimental and computational approaches across multiple levels—from molecules to tissues—to develop models that explain and predict cell behavior in human induced pluripotent stem cell (hiPSC) systems. All of the resources and tools generated in pursuit of this mission are shared openly with the scientific community. During this session, Allen Institute team members will present ongoing scientific projects using these tools to investigate changes in state of hiPSC derived endothelial cells exposed to shear stress, changes of state during the formation of 2D vs 3D structures in hiPSCs, and the use of neural networks to extract meaningful features in 3D microscopy data. In addition, Soah Lee from Sungkyunkwan University will present the use of our recent set of hiPSC derived disease cell line collections for cardiomyopathy. Finally, Sadao Ota from the University of Toyko will share the application of a recent Representation Learning framework to quantify interpretable measurements or representations of intracellular structures. The Allen Institute for Cell Science tools and resources shared in this session are openly available at our website.

Presenters and Talk Titles

Introduction to the Allen Institute for Cell Science
presented by Ru Gunawardane, PhD (Allen Institute for Cell Science)

Modeling Human Cardiac Development and Disease In Vitro: Insights from iPSCs, Engineering, and Collaboration
presented by Soah Lee, PhD (Sungkyunkwan University)

Live-cell microscopy & quantification to study cell state transitions in hiPSC-derived endothelial cells
presented by Becky Zaunbrecher, PhD (Allen Institute for Cell Science)

Adherent hiPSC lumenoids: a robust 3D platform for bridging cellular dynamics and multicellular organization
presented by Leigh Harris, PhD (Allen Institute for Cell Science)

Interpretable representation learning for 3D multi-piece intracellular structures using point clouds
presented by Gideon Dunster, PhD (Allen Institute for Cell Science)

3D image analysis of pooled multicellular systems
presented by Sadao Ota, PhD (The University of Tokyo)