Yuanxin Zhu, Bridget Carragher, and Clinton S. Potter
Center for Integrative Molecular Biosciences and Department of Cell Biology
The Scripps Research Institute, La Jolla, California, 92037
To expedite the development of fast and accurate algorithms and software tools for automatic particle selection and promote discussion about the state of the art techniques and technology, we held a two-day Multidisciplinary Workshop on Automatic Particle Selection for Cryo-electron microscopy (cryoEM), April 24-25, 2003, at the Center for Integrative Molecular Biosciences, The Scripps Research Institute, La Jolla, California. A total of 47 people attended the workshop, coming from Europe, Australia, Japan, and the United States. Representatives from both FEI Company and JEOL Ltd. participated in the workshop. The number of participants clearly underscored the intense and widespread interest in the subject of automatic particle selection within the rapidly expanding field of cryoEM. It also demonstrated the current focus on automation, which will be critical to the overall goal of high throughput molecular microscopy.
During the two-day workshop, we accomplished the two goals proposed in the workshop announcement (see: http://nramm.scripps.edu/seminars/2003/prtl_work/). First, representative interested researchers from multidisciplinary scientific communities were brought together at the workshop to exchange ideas, techniques, and software tools for automatic particle selection. Among the 14 speakers at the workshop were experts from the cyroEM community, including Timothy S. Baker, Robert M. Glaeser, Steven J. Ludtke, Pawel A. Penczek, Fred J. Sigworth, and several others; representatives from the computational geometry field, such as Chandrajit Bajaj, Marshall Bern, and Herbert Edelsbrunner; and acknowledged leaders in the field of computer vision and image processing, including David J. Kriegman and Ravi Malladi. In addition to the 14 oral presentations, 6 posters were also presented during a very well attended and lively poster session. Please refer to the workshop handbook for a full list of registered participants.
Toward the second goal of establishing a common ground to evaluate existing and future methods for automatic particle selection, a very productive discussion took place during a special session held in the afternoon of the first day. The discussion centered on both how to build benchmark particle datasets as well as how to setup criteria for evaluating a particular method of particle selection. A practical basis for the discussion was provided by a common dataset that had been distributed, over the web, to all participants before the workshop. Using this dataset 11 groups participated in a particle selection "bake-off" in which they used their own particular algorithms to select particles from this common dataset. The results of the selection were then tabulated and compared and served to focus the discussion. Participants agreed that establishing benchmark particles and using bakeoffs to compare methods are excellent ideas and that the infrastructure set up to support the Workshop bake-off should be maintained and extended to include larger and more varied datasets and more criteria for comparisons. The bakeoff participants also agreed to make their results publicly available to the rest of the scientific community and cooperate in publishing the results in a jointly authored paper.
Acknowledgements: Special thanks go to Cynthia Ona for her assistance. Many thanks to Arcy Arellano and the rest of the Automated Molecular Imaging group at the Scripps Research Institute for help provided before and during the workshop.
Financial support for the workshop was provided by the National Resource for Automated Molecular Microscopy which is supported by the National Institutes of Health though the National Center for Research Resources' P41 program (RR17573).