ArDean Leith

Computer Scientist

M.S.   Computer Science, Rensselaer Polytechnic Inst.
Ph.D. Biology (Biophysics), University of Rochester

Employed by: Div. of Computational Biology and Molecular Imaging, at Wadsworth Labs

Ardean (that's an ancient Scottish name) has been involved in advancing computational techniques in biological imaging since 1985. He initially set up a data base for serial-section imagery and developed computer graphics techniques for recovery of depth information from stereoscopic electron microscopy. He also developed techniques and software for visualizing and interacting with images from electron microscopes. More recently he has worked on techniques for speeding and parallelizing the computations involved in single particle reconstructions from electron micrographs. This work appears within the SPIDER image processing software. He writes and maintains a lot of Web based documentation. He also manages more than 90 computers used in this biological imaging research.

In a previous existence Ardean worked on Cellular Biology in a tropical Marine Biology Laboratory, taught in three Universities, and was greatly influenced by experience in the U.S Peace Corps.

Member of: Institute of Electrical and Electronics Engineers, Association for Computing Machinery; ACS; and the American Association for the Advancement of Science

Ardean is fluent in English and Malay (Malaysian/Indonesian) and understands a bit of Mandarin


Hsieh, C., A. Leith, C.A. Manella, J. Frank, and M. Marko. Toward high-resolution three-dimensional imaging of native mammalian tissue: Electron tomography of frozen-hydrated rat liver sections. J. Struct. Biol., 153, 1-13 (2006).

B.K. Rath, R. Hegerl, A. Leith, T.R. Shaikh, T. Wagenknecht, and J. Frank. Fast 3D motif search of EM density maps using a locally normalized cross-correlation function. J. Struct. Biol., 144, 95-103 (2003).

Hsieh, C.-E., Marko, M., Leith, A., Frank, J., and C.A. Manella. (2003) Electron tomographic comparision of frozen-hydrated and freeze-substituted sections of high pressure frozen rat-liver tissue. Microsc. Microanal. 8 (Suppl 2) 1178

Baxter, W. T., A. Leith, and J. Frank. (2002) A scripting language approach to control software for cryo-electron microscopy. The 2002 IEEE International Symposium on Biomedical Imaging. 301-305

Erlandsen, S.L., A.G. Bitterman, J. White, A. Leith, and M. Marko (2001) High resolution cryoFESEM of individual cell adhesion molecules (CAM) in the glycocalyx of human platelets: detection of P-selectin (CD62P), GPI-IX complex (CD42a/CD42ba,bb), and integrin GPIIbIIIa (CD41/CD61) by immunogold labeling and stereo imaging. J. Histochem. Cytochem. 49:809-819.

Spahn, C., P.A. Penczek, A. Leith, and J. Frank. (2000) A method for differentiating proteins from nucleic acids in itermediate-resolution density maps: cryo-electron microscopy defines the quaternary structure of the Escherichia coli 70S ribosome. Structure with Folding & Design 8:937-948.

Deng, Y., M. Marko, K.F. Buttle, A. Leith, M. Mieczkowski, and C.A. Manella. Cubic Membrane Structures in Amoeba Mitochondria Determined by Electron Microscopic Tomography. J. Structural Biol., 127, 231-239 (1999)

Li, Y., A. Leith, and J. Frank. Tinkerbell -- A Tool for Interactive Segmentation of 3D Data. J. Structural Biol., 120, 266-275 (1997)

Agrawal, R.K., P. Penczek, R.A. Grassucci, Y. Li, A. Leith, K.H. Nierhaus, and J. Frank. Direct Visualization of A-, P-, and E-Site Transfer RNAs in the Escherichia coli Ribosome. Science, 271, 1000-1002 (1996)

Marko, M. and A. Leith. Sterecon -- Three-Dimensional Reconstruction from Stereoscopic Contouring. J. Structural Biol., 116, 93-98 (1996)

J. Frank, M. Radermacher, P. Penczek, J. Zhu, Y. Li, M. Ladjadj, and A. Leith. SPIDER and WEB: Processing and Visualization of Images in 3D Electron Microscopy and Related Fields. J. Structural Biol., 116, 190-199 (1996)

Marko, M., A. Leith, K. Buttle and Y. Li. Contour-Based Segmentation and Visualization of Electron Tomographic Volumes. Proc. 53th Annual Meeting - Electron Micros. Soc., G. Bailey, ed. San Francisco Press, (1995)

Mannella, C.A., M. Marko, K. Buttle, P. Penczek, A. Leith, and J. Frank. Tomographic Reconstruction of Mitochondria. Proc. 53th Annual Meeting - Electron Micros. Soc., G. Bailey, ed. San Francisco Press, (1995)

Landis, W.J., M.J. Song, A. Leith, L. McEwen and B.F. McEwen. Mineral and Organic Matrix Interaction in Normally Calcifying Tendon Visualized in Three Dimensions by High-Voltage Electron Microscopic Tomography and Graphic Image Reconstruction. J. Struct. Biol., 110,39-54 (1993)

Summers, R.G., J.B. Morrill, A. Leith, M. Marko, D.W. Piston, and A.T. Stonebraker. A Stereometric Analysis of karyokinesis, Cytokinesis and Cell Arrangement During and Following Fourth Cleavage Period in the Sea Urchin. Development, Growth, and Differentiation 35,41-57 (1993)

Leith, A. Computer Visualization of Volume Data in Electron Tomography. In: Electron Tomography, J. Frank, ed., Plenum Publishing, NY. pp 215-236(1992).

Marko, M. and A. Leith. Contour-Based 3-D Reconstruction Using Stereoscopic Contouring and Digitized Images. In: New Dimensions of Visualization in Biomedical Microscopies, A. Kriete, ed., VCH Publishers, Weinheim. pp 45-73 (1992)

Marko, M., A. Leith, B. McEwen, J. Frank and C. Manella. Internal Compartmentation of the Mitochondirion: An HVEM Tomographic Study. Proc. 50th Annual Meeting - Electron Micros. Soc., G. Bailey, ed. San Francisco Press, 932-933 (1992)

Henick, D., M. Marko and A. Leith. 3-D Analysis of Murine Laryngeal Development. Proc. Ann. Mtg. Am. Larynogological Soc., Palm Springs, CA (1992)

Erlandsen, S.L., C.L. Wells, S.B. Olmsted, A. Leith and M. Marko. Applications of the STERECON System for the Determination of Area, Volume, and Linear Distance of Cell Surface Topography using Secondary and Backscattered Election Images in Low Voltage Field Emission SEM. Proc. 50th Annual Meeting - Electron Micros. Soc., G. Bailey, ed. San Francisco Press, 1320-1321 (1992)

Parsons, D.F., M. Marko and A. Leith. Organelle Rearrangement and Cell Volume Changes During Invasion of Peritoneal Elastic Lamina by Targeted Murine Breast Carcinoma Cells. Tissue and Cell, 23: 293-305 (1991)

Turner, J.W., D.H. Szarowski, K.L. Smith, M. Marko, A. Leith and J.W. Swann. Confocal Microscopy and Three-Dimensional Reconstruction of Electrophysiologically Identified Neurons in Thick Brain Slices. J. Electron. Micros. Tech., 18: 11-23 (1991)

Summers, R.G., E.E. Musial, P.C. Cheng, A. Leith and M. Marko. The Use of Confocal Microscopy and STERECON Reconstruction in the Analysis of Sea Urchin Embryonic Cell Division. J. Electron. Micros. Tech., 18: 24-30 (1991)

Parsons, D.F., A. Leith and M. Marko. The Relative Merits of Direct Morphology of Reconstruction of Whole Cells, and Statistical Morphometry by Stereology of Sections of Cells. Cell Biophysics, 17: 227-242 (1990)

Marko, M., A. Leith and D. Parsons. Advantages of Using Digitized for Serial-Section 3-D Reconstruction. Proc XIIth Int. Cong. for Electron Microscopy, San Francisco Press. 548-549 (1990)

Turner, J.W., D.H. Szarowski, K.L. Smith, M. Marko, A. Leith , J.W. Swann and R. Inman. Neurons in Thick Hippocampal Slices: Confocal Microscopy and Three-Dimensional Computer Reconstruction. Proc. XIIth Int. Cong. for Electron Microscopy, San Francisco Press. (1990)

Leith, A., M. Marko and D. Parsons. Computer Graphics for Cellular Reconstructions. IEEE Computer Graphics and Applications, 9(5): 16-23 (1989)

Marko, M., A. Leith and D. Parsons. Using Stereopair Images to Create 3-D Reconstructions from Serial Thick Sections. Europ. J. Cell Biol., Suppl. 25, 48: 161-164 (1989)

Marko, M., A. Leith and D. Parsons. Determination of Connections Between Cellular Structures Using 3-D Reconstruction from Multiple- View Stereopair Images of Thick Sections. Proc. 46th Annual Meeting Electron Micros. Soc. G. Bailey, ed. San Francisco Press, 28-29 (1988)

Marko, M., A. Leith and D. Parsons. Three-Dimensional Reconstruction of Cells From Serial Sections and Whole-Cell Mounts Using Multilevel Contouring of Stereo Micrographs. J. Electron Micros. Tech., 9: 395-411 (1988)

Marko, M., A. Leith and D. Parsons. Cell Morphology, Volume and Surface Area Determinations from Multiple Level Contouring Within HVEM Micrographs of Serial Sections and Whole Cell Mounts. Proc. 45th Annual Meeting - Electron Micros. Soc., G. Bailey, ed. San Francisco Press, 588-589 (1987)

Parsons, D.F., M. Marko, M. King, A. Leith and J. Frank. Computer Graphics HVEM Study of Perturbed Invading Carcinoma Cells. Proc. Am. Assoc. Cancer Res., April (1986)

Marko, M., R. Banerjee, A. Leith, M. King, M. Radermacher and D. Parsons. 3-D Reconstruction from Serial Thick Sections, with Multiple Level Profiling Within Stereo Pairs, Using Albany HVEM's "SSRECN" Software, Proc. 44th Ann. Meeting - Electron Micros. Soc., G. Bailey, ed. San Francisco Press, 38-39 (1986)

Leith, A. The Death of an Amoeba. J. Protozoology, 31: 177-180 (1984)

Leith, A. and M. C. Kaufman. Partial Purification of a Species-Specific Lethal Factor from Amoeba indica. J. Protozoology, 28: 121-123 (1981)

Leith, A. Variability of the Limited Lifespan State in Amoeba. Exp. Cell Research, 127: 261-267 (1980)

Leith, A. Role of Aggregation Factor and Cell Type in Sponge Cell Adhesion. Biol. Bull., 156: 212-223 (1979)

Leith, A. The Detection of Limited Life Span in Small Clones. J. Theor. Biol., 71: 453-464 (1978)

Leith, A. English-Bahasa Malaysia Scientific Dictionary. Universiti Kebangsaan Malyasia, Kuala Lumpur, Malaysia (1976)

The following two papers were reprinted in: Mathematical Models for Cell Rearrangements, G.D. Marstow, ed. Yale Univ. Press, 1975)

Leith, A. G. and N.S. Goel. Simulation of Movement of Cells During Self-Sorting. J. Theor. Biol., 33: 171-178

Goel, N.S. and A.G. Leith. Self-Sorting of Anisotropic Cells. J. Theor. Biol. 28: 469-482

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