A three-dimensional (M) version of the spectral signal-to-noise ratio (SSNR)-based resolution measure is introduced. The measure is defined for a class of 3D reconstruction algorithms that use interpolation in Fourier space. The statistical properties of the SSNR are discussed and related to the properties of another resolution measure, the Fourier shell correlation (FSC). The new measure was tested on 3D structures calculated from a simulated set of quasi-evenly spaced 2D projections using a nearest-neighbor interpolation and a gridding algorithm. In the latter case, the results agree very well with the FSC-based estimate, with the exception of very high SSNR values. The main applicability of the 3D SSNR is tomography, where due to the small number of projections collected, FSC cannot be used. The new measure was applied to three sets of tomographic data. It was demonstrated that the measure is sufficiently sensitive to yield theoretically expected results. Therefore, the 3D SSNR opens up the possibility of evaluating the quality of tomographic reconstructions in an objective manner. The 3D distribution of SSNR is of major interest in single-particle analysis. It is shown that the new measure can be used to evaluate the anisotropy of 3D reconstructions. The distribution of SSNR is characterized by three anisotropy indices derived from principal axes of the 3D inertia covariance matrix of the SSNR. These indices are used to construct a 3D Fourier filter which, when applied to a 3D reconstruction of a macromolecule, maximizes the SNR in real space and minimizes real-space artifacts caused by uneven distribution of 2D projections. (C) 2002 Elsevier Science (USA). All rights reserved.