An X-ray shadow projection microscope system using a scannable point source of X-rays is under development at AMIL-ARTS, SUNY at Buffalo, USA. The point source is generated by a focussed electron beam, which can be steered electromagnetically in a plane perpendicular to the optical axis of the microscope. A specimen is mounted on a rotatable mechanical stage for microtomography. Considering the hardware characteristics of this system and the limitations of current cone-beam reconstruction algorithms, a generalized Feldkamp’s cone-beam image reconstruction algorithm has been developed at our laboratories. In our cone-beam reconstruction, there are mainly two kinds of scanning scanning modes: planar and helix-like. A planar scanning locus is used to handle spherical or plate-like specimens. A typical case of planar scanning loci is a circle, which is used in Feldkamp’s cone-beam reconstruction. A helix-like scanning locus is used to deal with rod-shaped specimens. Without loss of generality, a locus turn of the X-ray source can be defined in cylindrical coordinates by the following equation: