The combination of optics and microfluidics is a very powerful and non invasive tool to perform single cell analysis and imaging. Being able to measure properties at a single cell level is of fundamental importance to understanding cellular systems and their heterogeneity. We present flow cytometry systems with added rotation techniques to gain isotropic high resolution 3D images of the measured objects. They can be combined with most optical microscopy systems and used with a wide range of fluorescent dyes and antibody staining.The optofluidic cell rotator (OFCR) holds single live cells in suspension using a dual beam optical trap and can rotate the cells by either manipulating the microfluidic flow or the alignment of the trapping beams. Such manipulations allow in plane, as well as tomographic rotation of the cell. By monitoring the cell during the smooth and controlled tomographic cell rotation, we can reconstruct a 3D image of the cell with an isotropic resolution, bypassing the normally lower z-resolution. Additionally, by measuring the nature of the rotation itself, it is also possible to observe underlying properties of the cells.We have explored a number of methods to perform cell rotation. One straightforward possibility is to flow liquid past the trapped cell. If the cell is held in the correct position, the imbalance of the forces acting across the cell surface results in a smooth tomographic rotation. We are able to show by cell rotation that the z-resolution can be improved by threefold over confocal imaging of the same cell. Another parameter which can be controlled is the relative position of the optical fibres, leading to a fibre-optic spanner. We have developed a novel dynamic fibre-optic spanner, capable of detailed measurement of the rotation properties of cells within the trap.