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

July 24th, 2015 @   - 

August 7 and 8, 2015.

Marine Biological Laboratory
Speck Auditorium, Rowe Building

Woods Hole, Massachusetts

The workshop will bring 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 will have two days of presentations and self-organized round table discussions among developers and users of 3D imaging technology.

Organizers: Rudolf Oldenbourg, Louie Kerr and Shalin Mehta

Workshop Registration Link

The program is organized in broad themes with contributions in the form of 20-minute presentations:

  1. The need for 3D imaging: Examples from biology
  2. Acquiring 3D data with light, electrons, X-rays, MRI: tomography, optical or mechanical sectioning, holography, light field
  3. Additional dimensions: time, wavelength, polarization, contrast agents
  4. Computational challenges: algorithms, computing resources, local versus cloud computing
  5. Visualization: Technology and concepts for presenting multidimensional data

Send inquiries to Rudolf, Louie, and Shalin

All lectures are held in the Speck Auditorium of the Rowe Buiding on the MBL campus

Friday, August 7
9:00 AM – 10:30 AM The need for 3D imaging: Examples from biology

Amy Gladfelter, Dartmouth College, how cells are organized in time and space

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

Scott Gallager, Woods Hole Oceanographic Inst., Monitoring fish populations in the ocean

James Weaver, Harvard U., Computer Tomography

Coffee Break 10:30 AM – 11:00 AM

11:00 AM – 12:30 Light microscopy: Three and more dimensions

Norbert Scherer, U. Chicago, ‘Insulin granule transport in a beta cell analog’

Shalin Mehta, MBL, ‘3D polarized fluorescence recorded with the confocal microscope’

Gary Tearney, Harvard Medical School, OCT, microOCT

Lunch 12:30 – 1:30 PM (Swope cafeteria)

1:30 PM – 3:00 PM Electron microscopy

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

Josh Morgan, Harvard U., Brain connectome

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

Bobby Kasthuri, Argonne Nat. Lab., ‘Towards complete maps of brains using synchrotron x-ray sources and serial electron microscopy’

Coffee Break 3:00 PM – 3:30 PM

3:30 PM – 5:00 PM 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’

5:00 PM – 6:00 PM Round table discussion
suggested topics:

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

Your suggestion…

Dinner 6:00 PM – 7:30 PM (Swope cafeteria)

After dinner: self organized break-out sessions, rooms available Saturday, August 8
9:00 AM – 10:30 AM 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’

Coffee Break 10:30 AM – 11:00 AM

11:00 AM – 12:30 PM 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’

Lunch 12:30 PM – 1:30 PM (Swope cafeteria)

1:30 PM – 3:30 PM 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, Mass. General Hospital, ‘3D Slicer, a free, open source software package for visualization and image analysis’

Mixer 3:30 PM – 5:00 PM

Some logistical information on the workshop is noted below:

The registration fee will be $140, which includes coffee breaks, meals, and a social on Saturday afternoon.

Workshop Registration Link

Travel and Accommodations:

Many participants will already be in Woods Hole for other reasons.

For those who travel to Woods Hole for this event, be aware that MBL housing is full this summer.

If you need to make hotel reservations, we recommend that you do it as soon as possible.

This is the Falmouth Chamber of Commerce website.

Here are places to stay in Woods Hole: Sleepy Hollow Motor Inn, Sands of Time Motor Inn, Woods Hole Inn.

All 3 hotels in Woods Hole are walking distance from the bus terminal and to the MBL.

Woods Hole can be reached by direct bus (Peter Pan) from Logan Airport and South Station in Boston.

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