CART: a controlled algebraic reconstruction technique for electron microscope tomography of embedded, sectioned specimen.

Reconstruction of thick, embedded, sectioned material has to cope with the restricted tilt view of the electron microscope, with information not stemming from the object of interest in the projections, with aberrations of the objective lens and with a distorted relationship between the projected densities in the micrographs and the specimen mass densities due to incoherent electron interactions within the specimen. Micrograph densities over a full tilt-range show in general an averaged mass increase which is more than should be expected from the cosine dependency of the tilt-angles of the projections. The hereby presented reconstruction technique finds a solution for the under-determined system by a controlled algebraic iteration procedure. For this solution the procedure stabilises the region of interest by dynamically scaling the input data during the procedure. A model for the electron transport through thick specimens is proposed and microscope projection simulations are carried out to test the algorithms.

Three-point repositioning of axes: three-dimensional alignment procedure for electron microscope tomography using three markers.

A description is given of a new procedure to align series of tilted graphs, made with an electron microscope, for computer tomographic purposes. The procedure uses the coordinates of three projected markers to calculate parameters needed for the reconstruction. To that end the procedure computes the direction of the tilt-axis, the translation and rotation parameters, the tilt-angle of every micrograph, and the spatial coordinates of the individual markers with their centre of gravity as origin of the coordinate system. A searching technique, based on cross-correlation, is described to locate accurately the micrographs markers.