Recent advances in optical microscopy have enabled biological imaging beyond the diffraction limit at nanometer resolution. A general feature of most of the techniques based on photoactivated localization microscopy (PALM) or stochastic optical reconstruction microscopy (STORM) has been the use of thin biological samples in combination with total internal reflection, thus limiting the imaging depth to a fraction of an optical wavelength. However, to study whole cells or organelles that are typically up to 15 m deep into the cell, the extension of these methods to a three-dimensional (3D) super resolution technique is required. Here, we report an advance in optical microscopy that enables imaging of protein distributions in cells with a lateral localization precision better than 50 nm at multiple imaging planes deep in biological samples. The approach is based on combining the lateral super resolution provided by PALM with two-photon temporal focusing that provides optical sectioning. We have generated super-resolution images over an axial range of Ϸ10 m in both mitochondrially labeled fixed cells, and in the membranes of living S2 Drosophila cells.nanoscopy ͉ PALM microscopy ͉ 3D imaging ͉ temporal focusing I nitial studies, based on defocusing (1), astigmatism (2), and others (3), have extended super resolution imaging (2, 4-13) to three dimensions (3D); however, only up to a few hundred nanometers in depth in biological samples. This is mainly due to the following: In photoactivated localization microscopy (PALM) (6, 12) and stochastic optical reconstruction microscopy (STORM) (8), a sufficient signal-to-noise ratio is required to discriminate single molecules from the background. In the defocusing approaches, background typically increases with imaging depth and the signal is further reduced as it is spread out across more pixels, making the signal to noise ratio insufficient for molecules that are more than a few hundred nanometers away from the focal plane. In addition, PALM is inherently a wide-field technique that is not well suited to point-scanning methods. The reason for this is 2-fold: First, in PALM, single molecules need to be imaged, that is, their emission has to be spread out across several pixels (6) and second, data are most efficiently collected when emissions from spatially segregated molecules are recorded in parallel-point-scanning methods are inherently serial, and are thus slower than wide-field methods (14).Thus, super resolution imaging would benefit greatly by adopting a wide-field technique and combining it with optical sectioning for enhanced signal to noise ratio at depth.In this article, we describe a method whereby a thin layer of photoactivatable fluorescent proteins (15) can selectively be activated in a location several micrometers deep in a cellular sample. This thin layer is then excited and imaged using the PALM technique with a demonstrated resolution of better than 50 nm. A succession of thin layer images can be combined to produce a volume image several micrometers in dep...