Multidisciplinary Workshop on Automatic Particle Selection for Cryo-electron Microscopy

April 24-25, 2003

Center for Integrative Biosciences (CIMBio)
The Scripps Research Institute (TSRI), La Jolla, California

Sponsored by the National Resource for Automated Molecular Microscopy (NRAMM)

Hosted by the National Resource for Automated Molecular Microscopy (NRAMM) and Department of Cell Biology at The Scripps Research Institute (TSRI)


Thursday April 24

7:30-7:45 AMShuttle service begins between Del Mar Inn and CIMBio, 15-20 minute roundtrip. Contact Del Mar Inn at (858) 755-9765
8:20 AMContinental Breakfast (Room 107, CIMBio)
8:50 AMNRAMM Overview
Bridget Carragher, The Scripps Research Institute
9:00 AMWelcome
Yuanxin Zhu, The Scripps Research Institute

Session 1 (Chair: Yuanxin Zhu)

9:10 AMHistorical background: Why are the simplest methods inadequate, and why is it important to do better?
Robert M. Glaeser
Department of Biochemistry & Molecular Biology, UC Berkeley
9:45 AMClassical Detection Theory and Error Bounds for the Particle Picking Problem
Fred J. Sigworth
Department of Cellular & Molecular Physiology, Yale University
10:20 AMCoffee Break and Leginon Demonstration
10:50 AMAnisotropic Filtering for Automatic Particle Selection
Chandrajit Bajaj
Department of Computer Science, University of Texas at Austin
11:25 AMSemi-automated Boxing of Images of Spherical Viruses: Two Approaches
Timothy S. Baker
Department of Biological Sciences, Purdue University
12:00 PMLunch on the west patio of CIMBio if weather permits; otherwise in the 2nd floor conference room.

Session 2 (Chair: Clinton S. Potter, The Scripps Research Institute)

1:00 PMMethods and Algorithms in Combinatorial Morse Theory
Herbert Edelsbrunner
Department of Computer Science, Duke University
1:35 PMAutomatic Particle Selection and CTF Parameterization with Integrated Database Access
Steve J. Ludtke
National Center for Macromolecular Imaging, Baylor College of Medicine
2:10 PMCoffee Break and Tour of CIMBio
2:40 PMDiscussion: Benchmark Particles, Datasets, Performance Metrics, and Future Directions
3:40 PMShort Break
3:50 PMA "Simple" Approach to Particle Picking
Ravi Malladi
Lawrence Berkeley National Laboratory, University of California
4:25 PMApplication of Template Matching Technique to Particle Detection in Electron Micrographs
Pawel Penczek
Department of Biochemistry and Molecular Biology, University of Texas-Houston
5:00 PMPoster Session (Beer will be served)
  1. Standard Conventions for Interchange and Archiving of Three-Dimensional Electron-Microscopy Data
    David M. Belnap (1), Mónica Chagoyen (2), J. Bernard Heymann (1)*
    (1) National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health. (2) Centro Nacional de Biotecnologia, Campus Universidad Autonoma.
  2. An automated Search and Evaluation System of TEM Image for Two-dimensional Crystal Screening of Membrane Protein
    Nakamura Natsuko, JEOL Ltd.
  3. A Two-step approach for Semi-automated Particle Selection from Low Contrast Cryo-electron Micrographs
    Richard Hall, Biochemistry Department, Imperial College, London
  4. SLEUTH -- a Fast Computer Program for Automatically Detecting Particles in Electron Microscope Images.
    Judith Short, MRC-Laboratory of Molecular Biology
  5. Hidden Markov Random Field Based Particle SelectionVivek Singh, Department of Computer Science, University of Central Florida
5:30 PMShuttle service back to Del Mar Inn by Sun Diego Charter (619) 299-2007
6:15 PMShuttle service from Del Mar Inn to Il Fornaio Restaurant (858) 755-8876
(4 blocks away, 10-15 minute walk).
6:30 PMDinner and Reception at Il Fornaio, 1555 Camino Del Mar, Del Mar, CA 92014. Tel: 858-755-8876. (See the map attached at the end of this handout).
9:00 PMShuttle service (Sun Diego Charter) back to Del Mar Inn.

Friday April 25

7:45-8:00 AMShuttle service begins between Del Mar Inn and CIMBio, 15-20 minute roundtrip.
8:30 AMContinental Breakfast (Room 107, CIMBio)

Session 3 (Chair: Bridget Carragher)

9:00 AMModel-based Particle Picking
Marshall Bern
Computer Sciences Lab, Palo Alto Research Center
9:35 AMAutomatic Particle Picking: A Two-stage Computational Framework
Yuanxin Zhu
Department of Cell Biology, The Scripps Research Institute
10:10 AMCoffe Break
10:35 AMDetecting Particles in Cryoelectron Micrographs: Lessons from Computer Vision and Pattern Recognition
David J. Kriegman
Department of Computer Science and Engineering, University of California at San Diego
11:10 AMParticle finding in electron micrographs using a fast local correlation algorithm
Alan Roseman
MRC - Laboratory of Molecular Biology
11:30 AMAutomated Particle Picking using Fast Local Correlation Search: A Spider procedure implementation
Bimal K. Rath
Wadsworth Center
11:50 AMSelecting Particles using Local Variance
Jasper R. Plaisier
Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University
12:10 PMClose Dicussion
12:15 PMLunch (grab and go lunchboxes) on the west patio of CIMBio if weather permits, otherwise, in 2nd floor conference room.
12:15 PMShuttle Service back to Del Mar Inn begins.

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