RASP: Optimal Single Puncta Detection in Complex Cellular Backgrounds.

Super-resolution and single-molecule microscopies have been increasingly applied to complex biological systems. A major challenge of these approaches is that fluorescent puncta must be detected in the low signal, high noise, heterogeneous background environments of cells and tissue. We present RASP, Radiality Analysis of Single Puncta, a bioimaging-segmentation method that solves this problem. RASP removes false-positive puncta that other analysis methods detect and detects features over a broad range of spatial scales: from single proteins to complex cell phenotypes. RASP outperforms the state-of-the-art methods in precision and speed using image gradients to separate Gaussian-shaped objects from the background. We demonstrate RASP's power by showing that it can extract spatial correlations between microglia, neurons, and α-synuclein oligomers in the human brain. This sensitive, computationally efficient approach enables fluorescent puncta and cellular features to be distinguished in cellular and tissue environments, with sensitivity down to the level of the single protein. Python and MATLAB codes, enabling users to perform this RASP analysis on their own data, are provided as Supporting Information and links to third-party repositories.

High-density volumetric super-resolution microscopy.

Volumetric super-resolution microscopy typically encodes the 3D position of single-molecule fluorescence into a 2D image by changing the shape of the point spread function (PSF) as a function of depth. However, the resulting large and complex PSF spatial footprints reduce biological throughput and applicability by requiring lower labeling densities to avoid overlapping fluorescent signals. We quantitatively compare the density dependence of single-molecule light field microscopy (SMLFM) to other 3D PSFs (astigmatism, double helix and tetrapod) showing that SMLFM enables an order-of-magnitude speed improvement compared to the double helix PSF by resolving overlapping emitters through parallax. We demonstrate this optical robustness experimentally with high accuracy ( > 99.2 ± 0.1%, 0.1 locs µm-2) and sensitivity ( > 86.6 ± 0.9%, 0.1 locs µm-2) through whole-cell (scan-free) imaging and tracking of single membrane proteins in live primary B cells. We also exemplify high-density volumetric imaging (0.15 locs µm-2) in dense cytosolic tubulin datasets.

Parabolic Potential Surfaces Localize Charge Carriers in Nonblinking Long-Lifetime "Giant" Colloidal Quantum Dots.

Materials for studying biological interactions and for alternative energy applications are continuously under development. Semiconductor quantum dots are a major part of this landscape due to their tunable optoelectronic properties. Size-dependent quantum confinement effects have been utilized to create materials with tunable bandgaps and Auger recombination rates. Other mechanisms of electronic structural control are under investigation as not all of a material's characteristics are affected by quantum confinement. Demonstrated here is a new structure-property concept that imparts the ability to spatially localize electrons or holes within a core/shell heterostructure by tuning the charge carrier's kinetic energy on a parabolic potential energy surface. This charge carrier separation results in extended radiative lifetimes and in continuous emission at the single-nanoparticle level. These properties enable new applications for optics, facilitate novel approaches such as time-gated single-particle imaging, and create inroads for the development of other new advanced materials.

Beyond the Threshold: A Study of Chalcogenophene-Based Two-Photon Initiators.

A series of nine soluble, symmetric chalcogenophenes bearing hexyl-substituted triphenylamines, indolocarbazoles, or phenylcarbazoles was designed and synthesized as potential two-photon absorption (2PA) initiators. A detailed photophysical analysis of these molecules revealed good 2PA properties of the series and, in particular, a strong influence of selenium on the 2PA cross sections, rendering these materials especially promising new 2PA photoinitiators. Structuring and threshold tests proved the efficiency and broad spectral versatility of two selenium-containing lead compounds as well as their applicability in an acrylate resin formulation. A comparison with commercial photoinitiators Irg369 and BAPO as well as sensitizer ITX showed that the newly designed selenium-based materials TPA-S and TPA-BBS outperform these traditional initiators by far both in terms of reactivity and dose. Moreover, by increasing the ultralow concentration of TPA-BBS, a further reduction of the polymerization threshold can be achieved, revealing the great potential of this series for application in two-photon polymerization (2PP) systems where only low laser power is available.

The excited-state dynamics of the radical anions of cyanoanthracenes.

The radical anion of 9,10-dicyanoanthracene (DCA) has been suggested to be a promising chromophore for photoredox chemistry, due to its nanosecond excited-state lifetime determined from indirect measurements. Here, we investigate the excited-state dynamics of the radical anion of three cyanoanthracenes, including DCA˙-, produced by photoinduced electron transfer in liquid using both pump-probe and pump-pump probe transient electronic absorption spectroscopy. All three excited radical ions are characterised by a 3-5 ps lifetime, due to efficient non-radiative deactivation to the ground state. The decay pathway most probably involves D1/D0 conical intersection(s), whose presence is favoured by the enhanced flexibility of the radical anions relative to their neutral counterparts. The origin of the discrepancy with the nanosecond lifetime of DCA˙-* reported previously is discussed. These very short lifetimes limit, but do not preclude, photochemical applications of the cyanoanthracene anions.

Sub-millisecond Translational and Orientational Dynamics of a Freely Moving Single Nanoprobe.

This paper presents a new experiment with which we are able to measure the 3D translational motion of a single particle at 10 µs time resolution and with ∼10 nm spatial resolution while at the same time determining the 3D orientation of the same single particle with 250 µs time resolution. These high time resolutions are ∼40 times greater than previous simultaneous measurements of 3D position and 3D orientation. Detailed numerical simulations and experiments are used to demonstrate that the technique can measure 3D orientation at the shot-noise limit. The microscope is also able to simultaneously measure the length or width (with the other assumed) of the plasmonic nanorods used here in situ and nondestructively, which should yield a greater understanding of the underlying dynamics. This technique should be applicable to a broad range of problems where environments which change in space and time may perturb physical and chemical dynamics.

Excited-state Dynamics of Radical Ions in Liquids.

Thomas Bally has acquired international recognition for his work on the photochemistry of reactive intermediates, which include radical ions. Here, we present a brief overview of our investigations of the excited-state dynamics of radical ions in liquids at room temperature, which are still poorly documented. A better understanding of these dynamics is most relevant, as open-shell ions in the excited state are being increasingly used in redox photochemistry and have been proposed to play a key role in highly exergonic photoinduced electron transfer reactions.

Leveraging lifetime information to perform real-time 3D single-particle tracking in noisy environments.

A microscopy platform that leverages the arrival time of individual photons to enable 3D single-particle tracking of fast-moving (translational diffusion coefficient of ≃3.3 µm2/s) particles in high-background environments is reported here. It combines a hardware-based time-gating module, which enables the rate of photon processing to be as high as 100 MHz, with a two-photon-excited 3D single-particle tracking confocal microscope to enable high sample penetration depth. Proof-of-principle experiments where single quantum dots are tracked in solutions containing dye-stained cellulose, are shown with tracking performance markedly improved using the hardware-based time-gating module. Such a microscope design is anticipated to be of use to a variety of communities who wish to track single particles in cellular environments, which commonly have high fluorescence and scattering background.

Information bounds in determining the 3D orientation of a single emitter or scatterer using point-detector-based division-of-amplitude polarimetry.

Determining the 3D orientation of a single molecule or particle, encoded in its polar and azimuthal angles, is of interest for a variety of fields, being relevant to a range of questions in elementary chemical reactivity, biomolecular motors, and nanorheology. A popular experimental method, known as division-of-amplitude polarimetry, for determining the real-time orientation of a single particle is to split the emitted/scattered light into multiple polarizations and to measure the light intensity using point detectors at these polarizations during a time interval Δt. Here, we derive the Cramér-Rao lower bounds for this method from the perspective of information theory in the cases of utilizing a chromophore or a scattering particle as a 3D orientation probe. Such Cramér-Rao lower bounds are new for using this experimental method to measure the full 3D orientation in both the scattering case and the fluorescence case. These results show that, for a scatterer, the information content of one photon is 1.16 deg-2 in the polar and 58.71 deg-2 in the azimuthal angles, respectively. For a chromophore, the information content of one photon is 2.54 deg-2 in the polar and 80.29 deg-2 in the azimuthal angles. In addition, the Cramér-Rao lower bound scales with the square root of the total signal photons. To determine orientation to an uncertainty of one degree requires 7.40 × 104 and 2.34 × 103 photons for the polar and the azimuthal angles, respectively, for fluorescence, whereas it takes 1.62 × 105 and 3.20 × 103 photons for scattering. This work provides experimentalists new guidelines by which future experiments can be designed and interpreted.

Two RuII Linkage Isomers with Distinctly Different Charge Transfer Photophysics.

The ligand PHEHAT (PHEHAT = 1,10-phenanthrolino[5,6-b]1,4,5,8,9,12-hexaazatriphenylene) presents a structural asymmetry that has a dramatic influence on the photophysical properties depending on the chelation site of the metal ion in the linkage isomers. While [RuII(phen)2HATPHE]2+ behaves classically, like [RuII(bpy)3]2+, [RuII(phen)2PHEHAT]2+ exhibits an unusual behavior. It appears that this complex has two 3MLCT bright states, the lower one being weakly emissive or nonemissive depending on the solvent and temperature. Different photophysical techniques involving a wide range of various temperatures and timescales are essential to analyze this difference. A full photophysical scheme is proposed based on experimental data and density functional theory calculations. While previous studies focused on high temperatures and longer timescale emission, we explore the complexes at very low temperatures and very short times in order to obtain a more complete picture of the intriguing photophysical behavior of these complexes.