Working Group 7: Multiscale Imaging

Working Group Lead: Yoonsuck Choe,

Goals and Objectives:

The goal of the working group is to facilitate (1) model and data sharing and (2) scientific collaboration among MSM members, on the issues of multiscale imaging and image analysis.

Working Group 7 Participants

Click on the section heading above to view the list of participants.

This working group is also linked with Working Group 3 Macro-To-Micro Scale Imaging and Transport in Biological Systems.


Currrent Discussion

May, 2007: See Working Group 3 for current discussions


Model Repository

External link: Initial set of data, for appreciation of other members' research area (6/15/06) (This site requires username/password. Please send email to Yoonsuck Choe ( for access.)



Tuesday June 23, 2009 4-5pm EDT - Stephen J. Smith, Stanford University

  • Title: Synapse Classification for Circuit Reconstruction: The Synaptome Meets the Connectome
  • Authors: Stephen J Smith, Kristina Micheva, JoAnn Buchanan, Nancy O’Rourke, Brad Busse, Nick Weiler.
  • Affiliation: Dept. of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305.

Useful circuit reconstruction requires the identification of circuit components as well as the abstraction of circuit connectivity diagrams. In reconstructing (or “reverse‐engineering”) human‐engineered circuits, the challenges of component identification are usually relatively inconsequential, because component diversity is small, and much is generally known in advance, including appropriate component classification schemes (e.g., mosfet, capacitor, etc.). In the case of neural circuits, however, the identification of component properties involves challenges that may be far more formidable. Both gene expression and physiological data suggest today that neural circuit components, such as synapses and dendrites, could be almost limitless in their molecular, structural and functional diversity.

We are using array tomography (Micheva & Smith, Neuron, 55:25‐36, 2007) to: (1) empirically define the extent of synapse molecular and structural diversity, (2) discover categories that encapsulate the major components of synapse diversity (i.e., a “Synaptome”), and, (3) identify a compact set of markers optimal to classify synapses during high‐throughput connectomic imaging. We have chosen rectangular slabs of mouse somatosensory cortex that extend through the entire cortical depth as a representative and amenable “microcosm” of CNS circuitry. We are using a panel of antibody markers chosen to identify synapse classes that might be based, for instance, on differing neurotransmitter receptor and transporter types. We anticipate that a synaptome will prove useful as a framework for the better understanding of the large‐scale circuit connectivity diagrams that will be connected in the years ahead by means such as KESM, and for better understanding the differential susceptibilities of subsets of neurons and synapses to neurodevelopmental and neurodegenerative disorders.

Supported by grants from the NIH (NS054252; NS063210), the McKnight Endowment Fund for Neuroscience, the Howard Hughes Medical Foundation, and the Gatsby Charitable Foundation.

YouTube videos: search for "TheSmithlab", one example: (choose HQ or HD option for best results)


Choe Breeze presentation to WG3 on 24 August 2007 entitled "Data Processing for Serial Sectioning Microscopy of Neural and Vascular Microstructure"

  • Links to movies shown during Choe's presentation
  1. KESM cutting
  2. Raw data and data fly-throughs
  3. 3D reconstruction

Wilson Breeze presentation to WG3 on 7 December 2007 entitled "Imaging Cells at Nanometer Resolution"

Current Events

Gulliver multiscale bioimaging workshop [1]

Friday December 7, 2007, 3:00 pm EST

Bridget Wilson presentation of her IMAG sponsored research in a WG7/WG3 Breeze conference

Title: Imaging Cells at Nanometer Resolution

Past Events

Society for Neuroscience 2008 Minisymposium on High-Throughput Microscopy and Computational/Theoretical Challenges in the Analysis of Neural Circuit Structure. Minisymposium archive (slides, etc.)

Chair: Louise C. Abbott, Co-chair: Yoonsuck Choe


Monthly Reports

Currently, the monthly reports below are simply hyper-links to external web pages. The reports will be gradually incorporated into the MSM wiki.




Journal Articles

  • Young, A; Frangi, A 'Computational Cardiac Atlases: from Patient to Population and Back' Experimental Physiology-Review Article 94.5 pp578-596 [Full text link]
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