System and method for nanoscale X-ray imaging of biological specimen. The imaging system comprises an X-ray source including a plurality of spatially and temporally addressable electron sources, an X-ray detector arranged such that incident X-rays are oriented normal to an incident surface of the X-ray detector and a stage arranged between the X-ray source and the X-ray detector, the stage configured to have mounted thereon a biological specimen through which X-rays generated by the X-ray source pass during operation of the imaging system. The imaging system further comprises at least one controller configured to move the stage during operation of the imaging system and selectively activate a subset of the electron sources during movement of the stage to acquire a set of intensity data by the X-ray detector as the stage moves along a three-dimensional trajectory.