A phasor-based approach to improve optical sectioning in any confocal microscope with a tunable pinhole

Exploiting the detector distance information in image scanning microscopy by phasor-based SPLIT-ISM

Confocal microscopy is an important bio-imaging technique that increases the resolution using a spatial pinhole to block out-of-focus light. In theory, the maximum resolution and optical sectioning are obtained when the detection pinhole is fully closed, but this is prevented by the dramatic decrease in the signal reaching the detector. In image scanning microscopy (ISM) this limitation is overcome by the use of an array of point detectors rather than a single detector. This, combined with pixel reassignment, increases the resolution of 2 over widefield imaging, with relatively little modification to the existing hardware of a laser-scanning microscope. Separation of photons by lifetime tuning (SPLIT) is a super-resolution technique, based on the phasor analysis of the fluorescent signal into an additional channel of the microscope. Here, we use SPLIT to analyze the information encoded within the array detectors distance for improving the resolution of ISM (SPLIT-ISM). We find that the lateral resolution can be increased of an additional 1.3 × with respect to the pixel-reassigned image with a concomitant increase in optical sectioning. We applied the SPLIT-ISM technique on biological images acquired by two currently available ISM systems: the Genoa Instruments PRISM and the Zeiss Airyscan. We evaluate the improvement provided by SPLIT-ISM through the QuICS algorithm, a quantitative tool based on image correlation spectroscopy. QuICS allows extracting three parameters related to the resolution, and contrast SNR of the image. We find that SPLIT-ISM provides an increase in spatial resolution for both the Genoa Instrument PRISM and the Zeiss Airyscan microscopes.

Combining a tunable pinhole with synchronous fluorescence spectrometry for visualization and quantification of benzo[a]pyrene at the root epidermis microstructure of Kandelia obovata

The adsorption of polycyclic aromatic hydrocarbons (PAHs) by mangrove roots and their transport to chloroplasts is a potentially critical process that reduces the carbon sequestration efficiency of mangroves. Yet the crucial initial step, the distribution and retention of PAHs at the root epidermis microstructure, remains unclear. A novel method with a spatial resolution of 311 nm was developed for visualizing and quantifying benzo[a]pyrene (B[a]P) at the root epidermis microstructure (0.096 mm2) of Kandelia obovata (Ko). This method combined a tunable pinhole in laser confocal scanning microscopy with synchronous fluorescence spectrometry to reduce the auto-fluorescence interference in locating B[a]P and improve quantitative sensitivity. The linear range for the established method was 0.44-50.00 ng mm-2, with a detection limit of 0.063 ng mm-2 and a relative standard deviation of 9.45%. In a 60-day hydroponic experiment, B[a]P was primarily adsorbed along the epidermis cell walls of secondary lateral roots and lateral roots, with retained amounts of 0.65 ng mm-2 and 0.49 ng mm-2, respectively. It was found to cluster and predominantly accumulate at the epidermal cell surfaces of taproots (0.24 ng mm-2). B[a]P might enter inner root tissues through the root epidermal cell walls and surfaces of Ko, with the cell walls potentially being the main route. This study potentially provides a pathway for visualizing and quantifying B[a]P entering inner root tissues of mangroves.

SPLIT-PIN software enabling confocal and super-resolution imaging with a virtually closed pinhole

In point-scanning microscopy, optical sectioning is achieved using a small aperture placed in front of the detector, i.e. the detection pinhole, which rejects the out-of-focus background. The maximum level of optical sectioning is theoretically obtained for the minimum size of the pinhole aperture, but this is normally prevented by the dramatic reduction of the detected signal when the pinhole is closed, leading to a compromise between axial resolution and signal-to-noise ratio. We have recently demonstrated that, instead of closing the pinhole, one can reach a similar level of optical sectioning by tuning the pinhole size in a confocal microscope and by analyzing the resulting image series. The method, consisting in the application of the separation of photons by lifetime tuning (SPLIT) algorithm to series of images acquired with tunable pinhole size, is called SPLIT-pinhole (SPLIT-PIN). Here, we share and describe a SPLIT-PIN software for the processing of series of images acquired at tunable pinhole size, which generates images with reduced out-of-focus background. The software can be used on series of at least two images acquired on available commercial microscopes equipped with a tunable pinhole, including confocal and stimulated emission depletion (STED) microscopes. We demonstrate applicability on different types of imaging modalities: (1) confocal imaging of DNA in a non-adherent cell line; (2) removal of out-of-focus background in super-resolved STED microscopy; (3) imaging of live intestinal organoids stained with a membrane dye.

Alterations induced by the PML-RARα oncogene revealed by image cross correlation spectroscopy

The molecular mechanisms that underlie oncogene-induced genomic damage are still poorly understood. To understand how oncogenes affect chromatin architecture, it is important to visualize fundamental processes such as DNA replication and transcription in intact nuclei and quantify the alterations of their spatiotemporal organization induced by oncogenes. Here, we apply superresolution microscopy in combination with image cross correlation spectroscopy to the U937-PR9 cell line, an in vitro model of acute promyelocytic leukemia that allows us to activate the expression of the PML-RARα oncogene and analyze its effects on the spatiotemporal organization of functional nuclear processes. More specifically, we perform Tau-stimulated emission depletion imaging, a superresolution technique based on the concept of separation of photons by lifetime tuning. Tau-stimulated emission depletion imaging is combined with a robust image analysis protocol that quickly produces a value of colocalization fraction on several hundreds of single cells and allows observation of cell-to-cell variability. Upon activation of the oncogene, we detect a significant increase in the fraction of transcription sites colocalized with PML/PML-RARα. This increase of colocalization can be ascribed to oncogene-induced disruption of physiological PML bodies and the abnormal occurrence of a relatively large number of PML-RARα microspeckles. We also detect a significant cell-to-cell variability of this increase of colocalization, which can be ascribed, at least in part, to a heterogeneous response of the cells to the activation of the oncogene. These results prove that our method efficiently reveals oncogene-induced alterations in the spatial organization of nuclear processes and suggest that the abnormal localization of PML-RARα could interfere with the transcription machinery, potentially leading to DNA damage and genomic instability.