Table 1.

Examples of super-resolution microscopy and their application to study nuclear processes and structures.

Type of microscopy	Mechanism of action	Application to imaging nuclear structures
Stimulated emission depletion (STED)	Enhances resolution by depleting fluorescence in specific regions of the sample while leaving a center focal spot active to emit fluorescence. This is achieved by generating a “doughnut” around the focal spot using a second depletion laser beam.	• γ-H2AX foci colocalizing with Ku foci160 • Mobility of proteins being imported into the nucleus161
Spatially modulated illumination (SMI)	Spatially modulated illumination (SMI) microscopy achieves higher spatial resolution by modulating the illuminating light along the optical axis, after which the sample is moved through a standing wave field at precise axial steps. This technique provides improved z-axis resolution for each of the fluorophores162	• Chromatin compaction of specific loci163 • Live cell measurements of a tet-operator repeat insert in U2OS cells164
Structured illumination microscopy (SIM)	Similar to SMI in that it generates a spatially modulated illumination pattern; however this occurs along the object plane (x,y) rather than the optical (z) plane165. Multiple images are acquired and then computationally combined to generate an image with twice the resolution as traditional widefield microscopy165.	• RecA bundle formation and localization166 • NPCs colocalization with channels in the lamin network and peripheral heterochromatin167
Photo-activated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM)	Identify precise locations of individual fluorophores by using photoswitchable fluorophores to achieve optical isolation of the signal168.	• Volume of chromatin in different epigenetic states169 • H2B localization in interphase cells170