The four goals of the BioImage Database project were: (I) to provides a searchable database and archive for digital images of biological specimens obtained by any form of microscopy, (ii) to allow such images to be collected, stored and organized, (iii) to make the images and their metadata available electronically via the Internet for personal study, educational and scientific research purposes, (iv) and to provide tools to assist in the downloading and visualization of such images, and in making comparisons between them. These goals have been reached within the third period of the project. Dr. Shotton, University of Oxford has now taken charge of the continuation of this project together with Ingenta LTD (http://www.ingenta.com).
The Basel and SGI groups have provided extensions to current web-based technology that allow effective volume data management, visualization and comparison. Within the third period of the BioImage project the Basel group has developed the tools for converting many types of currently used image formats, and to manipulate and display three-dimensional (3D) image data. These tools comprise a large set of format converters and 3D rendering modes. They have been thoroughly tested among the groups in the project and can be downloaded from our website
http://www.mih.unibas.ch/Homepages/heymann/Bsoft.html. We have exploited these tools in several projects that required comparison of 3D structural information with surfaces topographs recorded by atomic force microscopy (AFM). First, we have compared the various atomic models of bacteriorhodopsin (BR) elucidated by electron and x-ray crystallographies with data from AFM [1]. This work demonstrates the problems of accessing information of the loops connecting plausibility.
In a second work, this method was extended to structure prediction [2]. The functionally important loop of rhodopsin (R) was grafted to BR and topographs recorded. Many models of the R-EF were built and equilibrated by molecular dynamic simulations and subsequently tested with the topograph. In this way, a preliminary model of this loop was established.
1. Heymann, J.B., J.D. Müller, E.M. Landau, J.P. Rosenbusch, E. Pebay-Peyroula, G. Büldt and A. Engel (1999). Charting the surfaces of the purple membrane. J. Struct. Biol. 128, 243-249.
2. Heymann, J.B., M. Pfeiffer, V. Hildebrandt, H.R. Kaback, D. Fotiadis, B. de Groot, A. Engel, D. Oesterhelt and D.J. Müller (2000). Conformations of the rhodopsin third cytoplasmic loop grafted onto bacteriorhodopsin. Structure in press.
