CNS*2010 Workshop

High-throughput 3D microscopy and high-performance computing for multi-scale modeling and simulation of large-scale neuronal circuits

July 30, 2010, San Antonio, TX

Schedule: 8:30am 9:00am to 4:30pm 5:00pm [NEW: schedule summary]
NOTE: the workshop will begin at 9:00am!
Mahncke Room, 3rd floor, Sheraton Gunter Hotel

Organizers: Yoonsuck Choe, John Keyser, and Louise C. Abbott
Brain Networks Laboratory, Texas A&M University

Synopsis: Rapid advances in high-throughput, high-volume 3D microscopy technology is enabling the acquisition of neuronal-level data at the scale of whole small animal organs such as the mouse brain. Techniques that allow 3D molecular imaging and ultra high-resolution electron microscopy imaging provide a complementary perspective, where detailed local circuit function can be investigated. These microscopy technologies, together with high-performance computing power becoming available are enabling a data-driven, multi-scale modeling and simulation of large-scale neuronal circuits (such as the complete connectome of the mouse). This workshop will give a timely update on this burgeoning field and provide a forum for intensive discussion to shape the immediate and future direction of data-driven computational modeling and simulation of the brain.

This workshop is organized in memory of the late Bruce H. McCormick (1928–2007, SfN member obituary), inventor of the Knife-Edge Scanning Microscope and a pioneer in scientific visualization. (Also see the Society for Neuroscience minisymposium we organized in 2008.)

Organization for Computational Neuroscience


This will be a day-long workshop, with the program consisting of the talks listed below, plus an hour-long panel discussion where everyone is encouraged to participate.

Confirmed talks : Abstracts are now online. First authors will give the presentation.

  • [9:00am] Introduction

    [PDF slides]

  • [9:10am] Louise C. Abbott, David Mayerich, Jaerock Kwon*, and Yoonsuck Choe (Texas A&M University, *Kettering University)

    High-throughput imaging of whole mouse brain using the Knife-Edge Scanning Microscope


  • [9:35am] Kenneth J. Hayworth, Narayanan Kasthuri, Richard Schalek, Juan C. Tapia, Jeff Lichtman (Harvard University)

    Large Volume Neural Circuit Reconstruction Using the Tape to SEM Process


  • [10:00am] Daniel Berger and H. Sebastian Seung (MIT)

    Semi-automatic SEM imaging and analysis of neuronal connectivity using ATLUM/ATUM slice stacks


  • [10:25am] Coffee break

  • [10:35am] Brad Busse, Kristina Micheva, and Stephen J. Smith (Stanford University)

    Large scale synaptic analysis with Array Tomography


  • [11:00am] Pablo Blinder1, Philbert S. Tsai1, John Kaufhold2, and David Kleinfeld1 (University of California, San Diego1 and SAIC2)

    Reconstruction of the cortical vascular network in mouse


  • [11:25am] Chris Bjornsson and Badri Roysam (RPI)

    Mapping the Glio-vascular Infrastructure of Brain Tissue


  • [12:15pm] Lunch break

  • [1:30pm] David Mayerich1, Yoonsuck Choe2, and John Keyser2 (1University of Illinois, Urbana-Champaign and 2Texas A&M University)

    Segmentation and Visualization of High-Throughput Microscopy Datasets


  • [1:55pm] Randal Koene (Fatronic Tecnalia Foundation, San Sebastian, Spain)

    Using new in-vivo techniques to add function to reconstructions from high-throughput micrsocopy


  • [2:20pm] Andrew Duchowski (Clemson University)

    Eye-tracking technology and its potential application to tracing and validation of microscopy data


  • [2:45pm] Todd Huffman (3Scan) and Peter Eckersley (Electronic Freedom Foundation)

    Large-scale, collaborative scanning, and the role of commercialization (tentative title)


  • [3:10pm] Coffee break

  • [3:35pm] Yoonsuck Choe (Texas A&M University) and Jaerock Kwon (Kettering University)

    Open issues in high-fidelity simulation of the connectome

    [Abstract] [PDF slides]

  • [4:00pm] Panel

    [PDF slides]

* First author will give the presentation. Some titles are tentative.

Schedule summary:

start	       duration		
09:00:00 AM	00:10	Intro	
09:10:00 AM	00:25	Abbott	
09:35:00 AM	00:25	Hayworth	
10:00:00 AM	00:25	Berger	
10:25:00 AM	00:10	> coffee break
10:35:00 AM	00:25	Busse	
11:00:00 AM	00:25	Blinder	
11:25:00 AM	00:50	Bjornsson keynote
12:15:00 PM	01:15	> lunch
01:30:00 PM	00:25	Mayerich	
01:55:00 PM	00:25	Koene	
02:20:00 PM	00:25	Duchowski	
02:45:00 PM	00:25	Huffman	
03:10:00 PM	00:25	> coffee break
03:35:00 PM	00:25	Choe	
04:00:00 PM	01:00	> Panel
05:00:00 PM			


  • 3Scan
  • Organization for Computational Neuroscience (OCNS)
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