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Journal of Electron Microscopy 48(3): 277-287 (1999)
© 1999 Oxford University Press

Automatic acquisition of fiducial markers and alignment of images in tilt series for electron tomography

David Ress, Mark L. Harlow, Mikael Schwarz1, Rober M. Marshall and Uel J. McMahan*

Department of Neurobiology, Stanford University School of Medicine Stanford, CA 94305, USA

*To whom correspondence should be addressed. E-mail: ujmcmahan{at}stanfoed.edu

Three-dimensional reconstruction of a section of biological tissue by electron tomography requires precise alignment of a series of two-dimensional images of the section made at numerous successive tilt angles. Gold beads on or in the section serve as fiducial markers. A scheme is described that automatically detects the position of these markers and indexes them from image to image. The resulting set of position vectors are arranged in a matrix representation of the tilt geometry and, by inversion, alignment information is obtained. The scheme is convenient, requires little operator time and provides an accuracy of <2 pixels RMS. A tilt series of 60–70 images can be aligned in –30 min on any modern desktop computer.

Keywords     electron microscopy, electron tomography, fine structure

Received      8 February 1998, accepted 8 March 1999


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