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Name of Collaboratory :

Collaboratory for Microscopic Digital Anatomy (CMDA)

URL :

Collaboratory Status :

Completed

Start Date : 1994

End Date : 1999

Primary Collaboratory Function :

Shared Instrument

Secondary Collaboratory Functions :

Expert Consultation

Domain(s) :

Anatomical Telemicroscopy, Tomography

Brief Description of the Collaboratory :

The Collaboratory for Microscopic and Digital Anatomy (CMDA), also termed "Telemicroscopy," was a major research initiative to create online access to the intermediate-high voltage electron microscope (IVEM) at the National Center for Microscopy and Imaging Research (NCMIR) so that researchers could run the microscope from remote workstations. This project also consisted of access to high performance computing to derive three-dimensional datasets of biological structure from IVEM images using electron tomography, and mechanisms for remote visualization and analysis of three-dimensional data.

As of the August 1, 1997, the CMDA project was formally recognized as a component of San Diego Supercomputer Center (SDSC).

Access to Instruments :

Intermediate-high voltage transmission electron microscope (with Java web interface to CMDA 2.0 software and VidCon)

Access to Information Resources :

Database of shared session images (simultaneously viewable by collaborators)

Access to People as Resources :

Microscope control hand-off between researchers within a session, telephone communication between researcher(s) and microscope operator

Funding Agency or Sponsor :

Datacube, Inc

United States Department of Health and Human Services

National Institutes of Health (NIH)

National Science Foundation (NSF)

Photometrics LTD

Silicon Graphics, Inc. (SGI)

State of California

Sun Microsystems Computer Corp.

University of California System (UC System)

Notes on Funding Agencies/Sponsors:

TOTAL PARTICIPANTS:

Notes on Participants/Organizations:
12 people total working on the design and development of the system including the PI's and the management layer: 2-3 actual application developers per site, as well as the PI's and the project managers.
5-10 different people over a period of a few years

Communications Technology Used :

The collaborators have text messanging during the sessions, as well as shared visualizations of the slides that can double as a shared whiteboard for annotation with reference pointers. Because of the original low quality of the video feed and lack of feedback, initial focusing by distributed collaborators was difficult; they often had an onsite technician do the initial focusing of the specimen. Later refinements also incorporated some auto-focusing mechanisms.

Technical Capabilities :

Management of technical resources
Access control/login facilities
Computation
Simulation, modeling, visualization
Asynchronous object sharing
General search capability, Vetted knowledge based of multiple authors, Data stream capture
Asynchronous conversation
Email
Synchronous object sharing
Telepointers/annotation, Instrument monitoring, Shared instrument control, Electronic whiteboards, Share visualization
Synchronous conversation
Audio, Instant messaging/chat

Key Articles :

Finholt, T. A. (2003). Collaboratories as a new form of scientific organization Economics of Innovation and New Technology, 12(1), 5-25.

Finholt, Thomas A. (2002). Collaboratories: Science over the Internet. in Teich, Albert H., Nelson, Stephen D., and Lita, Stephen J. (editors). AAAS Science and Technology Policy Yearbook. (pp. 339-344). Washington, DC: American Association for the Advancement of Science.

Hadida-Hassan, M., Young, S. J., Peltier, S. T., Wong, M., Lamont, S., & Ellisman, M. H. (1999). Web-based telemicroscopy. Journal of Structural Biology, 125, 235-245.

Kouzes, R. T. (2000). Electronic collaboration in environmental and physical sciences research. In S. H. Koslow & M. F. Huerta (editors). Electronic collaboration in science. (pp. 89-112). Mahwah, NJ: Lawrence Erlbaum.

Young, S. J., Fan, G. Y., Hessler, D., Lamont, S., Elvins, T. T., Hadida-Hassan, M., Hanyzewski, G. A., Durking, J. W., Hubbard, P., Kindlmann, G., Wong, E., Greenberg, D., Karin, S., & Ellisman, M. H. (1996). Implementing a collaboratory for microscopic digital anatomy. International Journal of Supercomputing Applications and High Performance Computing, 10(2/3), 170-181.

Project-reported performance data :

Images of the Collaboratory:

screen shot

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This material is based upon work supported by the National Science Foundation under Grant No. IIS 0085951. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

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