BS-C-1 cells (ATCC) were fixed, immunostained with rabbit anti-Tom20 (Santa Cruz Biotech) and/or mouse anti-β-tubulin (TUB2.1, Cytoskeleton) (See Supplementary Methods online for the detailed immunostaining procedure). The stained cells were imaged in PBS with the addition of 100 mM mercaptoethylamine at pH 8.5, 5% glucose (w/v) and oxygen scavenging enzymes (0.5 mg/mL glucose oxidase (Sigma-Aldrich), and 40 μg/mL catalase (Roche Applied Science)), unless otherwise mentioned. This above imaging buffer has a refractive index of 1.34. Media with higher refractive index (1.45) based on 80% (v/v) glycerol and 5% (w/v) glucose, or 60% (w/w) sucrose solution and 5% (w/w) glucose, were used in some experiments, both with the same amount of mercaptoethylamine and oxygen scavenging enzymes as described above. The slight mismatch between the medium refractive index and coverglass is needed for focus locking during imaging. Although a high concentration of mercaptoethylamine and oxygen scavenging system were used here for fixed cell imaging, the cyanine dyes also switch in buffers with lower concentrations of thiol and oxygen scavenger system compatible with live cell imaging12 (link).
Data acquisition was performed on a fluorescence microscope as described in theSupplementary Methods online. Specifically for 3D imaging, a cylindrical lens with a focal length of 1 m was inserted into the imaging optical path for 3D localization8 (link). To stabilize the microscope focusing during data acquisition, the reflected excitation laser from the coverglass-medium interface was directed to a quadrant photodiode. The position read out of the quadrant photodiode, which was sensitive to the distance between the coverglass and the objective focal plane, was used to provide feedback to a piezo objective positioner (Nano-F100, MadCity Labs), allowing compensation for the focus drift. The residual drift, < 40 nm (Supplementary Fig. 7 online), was corrected during data analysis. For whole cell imaging in an aqueous medium, the objective positioner was stepped in 300 nm intervals, which corresponds to a focal plane displacement of 216 nm after correcting for the refractive index mismatch at the glass-medium interface. Molecules within 270 nm below the focal plane were accepted for image reconstruction. Whole cell images were obtained from 9 partially overlapped z-slices. For imaging in media with a refractive index of 1.45, the positioner was stepped in 650 nm intervals, corresponding to an actual focal plane displacement of 580 nm. Molecules within 360 nm above and below the focal plane are accepted and whole cell images were obtained from 4 partially overlapped z-slices.
For single color imaging, the A405-Cy5 labeled sample was continuously illuminated with a 657 nm imaging laser (~30 mW). A low intensity 405 nm laser was used to activate the probes, with intensity adjusted such that only an optically resolved subset of the probes were activated at any given time. In certain cases, the 405 nm laser can be omitted because the 657 nm laser can also activate Cy5, albeit at a low rate. Emission from the fluorophores were recorded by the camera at a frame rate of 20 Hz. 3D localization of individual molecules was performed as described previously8 (link) and described in theSupplementary Methods online. Multicolor imaging was performed by illuminating the sample repetitively with each frame of an activation laser followed by 3 frames of the 657 nm imaging laser. An alternating sequence of two activation lasers was used for two-color imaging. The 405 nm, 460 nm and 532 nm lasers were used to activated A405-Cy5, A488-Cy5, and A555-Cy5, respectively. Subtraction of crosstalk between different color channels were performed during data analysis as described in the Supplementary Methods online.
Data acquisition was performed on a fluorescence microscope as described in the
For single color imaging, the A405-Cy5 labeled sample was continuously illuminated with a 657 nm imaging laser (~30 mW). A low intensity 405 nm laser was used to activate the probes, with intensity adjusted such that only an optically resolved subset of the probes were activated at any given time. In certain cases, the 405 nm laser can be omitted because the 657 nm laser can also activate Cy5, albeit at a low rate. Emission from the fluorophores were recorded by the camera at a frame rate of 20 Hz. 3D localization of individual molecules was performed as described previously8 (link) and described in the