Escaping Flatland Workshop 2015, Summary

MBL Workshop Escaping Flatland: Imaging biological architecture and events in 3 dimensions.


August 7 and 8, 2015.

Marine Biological Laboratory
Speck Auditorium, Rowe Building

Woods Hole, Massachusetts

The workshop brought together researchers who work at the interface of biology, biochemistry, physics, engineering, and computer science to advance both sides of the coin, the technology of 3D imaging and its applications in biology. We had two days of presentations and self-organized round table discussions among developers and users of 3D imaging technology.

Organizers: Rudolf Oldenbourg, Louie Kerr, Shalin Mehta, and James Michaelson

Workshop Survey

Send inquiries to Rudolf, or Louie

List of Themes and 20-minute Presentations in chronological order:

Friday, August 7

The need for 3D imaging: Examples from biology

Amy Gladfelter, Dartmouth College, ‘How cells sense their own shape’

Thomas Mueller-Reichert, TU Dresden, ‘3D reconstruction of spindle organization and chromosome segregation’

Scott Gallager, Woods Hole Oceanographic Inst., ‘Applications of 3D imaging in oceanography’

James Weaver, Harvard U., ‘New Electron Microscopy Imaging Techniques for the Large-Scale High-Throughput Characterization of Hierarchical Biological Materials and Synthetic Constructs’

Light microscopy: Three and more dimensions

Shalin Mehta, MBL, ‘Probing molecular order in 3D with the confocal LC-PolScope’

Alex Valm, NICHD/NIH, ‘Live cell spectral imaging to deconstruct the organelle interactome’

Gary Tearney, Harvard Medical School, ‘Microimaging: Seeing the unseen in living patients’

Electron microscopy

Eduardo Rosa-Molinar, U. Kansas, ‘Serial block-face imaging revisited’

Josh Morgan, Harvard U., ‘Mapping a circuit from synaptic structure to network structure using large scale electron microscopy’

Shigeki Watanabe, U. Utah, ‘4-D electron microscopy’

Multifocus and light field microscopy

Sara Abrahamsson, Rockefeller U., ‘Multifocus microscopy – instant 3D imaging at full optical resolution’

Logan Grosenick, Stanford U., ‘Light field microscopy for functional imaging in neuroscience’

Michael Broxton, Stanford U., ‘Large-scale deconvolution algorithms, GPUs, and cloud computing’

Rudolf Oldenbourg, MBL, ‘Polarization and the 4-dimensional light field’

Round table discussion

Quantifying performance and resolution limits

Building community: towards an annual workshop and/or student course

3D display technology for the seminar and science class room

After dinner: self organized break-out session

Light field imaging

Saturday, August 8

Synchrotron and X-ray tomography, micro-CT

Jim Michaelson, Harvard Medical School, ‘Role of micro-CT in 3D pathology and anatomy’

Doga Gursoy, Argonne Nat. Lab., ‘Multidimensional imaging with synchrotron light’

Liang Gao, Stony Brook U., ‘Pushing the envelope of 3D live fluorescence imaging by selective plane illumination microscopy’

Light sheet microscopy

Hari Shroff, NIBIB/NIH, ‘Dual-view light-sheet microscopy for rapid, spatially isotropic 4D imaging of living cells and embryos’

Patrick La Riviere, U. Chicago, ‘Modeling and reconstruction for multi-view selective plane illumination microscopy.’

Daniel Colon-Ramos, Yale U., ‘WormGUIDES, towards the living connectome: systematic single cell analyses of neurodevelopment’

Raju Tomer, Stanford U., ‘Integrated high-resolution, high-throughput structural and functional mapping of large intact nervous systems’

Visualization: Technology and concepts for presenting multidimensional data

Mark Hereld, Argonne Nat. Lab., ‘Small Worlds: multi-modal 3D imaging’

Amanda Petford-Long, Argonne Nat. Lab., ‘Integrated Imaging – the Sum is Greater than the Parts’

Eva Dyer, Northwestern U., ‘From single cells to brain areas: Multi-scale models for visualizing 3D brain structure’

Rich Stoner, Synthego, ‘3D Visualization of laminar architecture in human neocortex’

Steve Pieper, Isomics, Inc., ‘3D Slicer, a free, open source software package for visualization and image analysis’

Gallery of images provided by workshop participants:


Group Photo

Source: Hari Shroff

Source: Steve Pieper


Selected presentation videos:


Source: MBL Videos

Source: MBL Videos

Source: MBL Videos