Motion of an object of interest, such as a cell, has a variable velocity that can be varied on a cell-by-cell basis. Cell velocity is controlled in one example by packing cells into a capillary tube, or any other linear substrate that provides optically equivalent 360 degree viewing access, so that the cells are stationary within the capillary tube, but the capillary tube is translated and rotated mechanically through a variable motion optical tomography reconstruction cylinder. The capillary tube motion may advantageously be controlled in a start-and-stop fashion and translated and rotated at any velocity for any motion interval, under the control of a computer program. As such, there are several configurations of the optical tomography system that take advantage of this controlled motion capability. Additionally, the use of polarization filters and phase plates to reduce light scatter and diffraction background noise is described.