We are developing two novel technologies, cryo soft x-ray tomography and cryo confocal fluorescence tomography, to obtain high-resolution maps of the position of molecules in cells. The first technology, soft x-ray tomography (SXT), is similar in concept to the well-established medical diagnostic technique computed axial tomography (CAT), except with SXT we obtain images at 50 nm isotropic resolution. With SXT we image unfixed, unstained cells and visualize structures based on the their absorption of x-rays. This is done by using photons with energies between the K shell absorption edges of carbon (284 eV, λ=4.4 nm) and oxygen (543 eV, λ=2.3 nm), where photons readily penetrate the aqueous environment while encountering significant absorption from carbon- and nitrogen-containing organic material.  Since organic material absorbs approximately an order of magnitude more strongly than water, we obtain a unique and quantifiable natural contrast image of cellular structures. X-ray absorption follows Beer’s Law, therefore the absorption of photons is linear, and a function of the biochemical composition at each point in the cell. The second technology, cryo confocal fluorescence tomography, allows us to localize specific molecules (e.g. tagged with genetically encoded proteins) in unfixed cells. We use cryo-immobilization to assure that the molecules are in the same position in cells that are sequentially imaged with fluorescence then x-ray microscopy, and tomographic procedures to achieve isotropic resolution. We then overlay the fluorescence data on the x-ray data to obtain 3D views of the positions of molecules with respect to cellular structures throughout the entire intact cell.