Deep learning multi-shot 3D localization microscopy using hybrid optical-electronic computing.

Current 3D localization microscopy approaches are fundamentally limited in their ability to image thick, densely labeled specimens. Here, we introduce a hybrid optical-electronic computing approach that jointly optimizes an optical encoder (a set of multiple, simultaneously imaged 3D point spread functions) and an electronic decoder (a neural-network-based localization algorithm) to optimize 3D localization performance under these conditions. With extensive simulations and biological experiments, we demonstrate that our deep-learning-based microscope achieves significantly higher 3D localization accuracy than existing approaches, especially in challenging scenarios with high molecular density over large depth ranges.

Characterization of the cholesterol efflux of apolipoprotein E-containing high-density lipoprotein in THP-1 cells.

High-density lipoprotein (HDL), also known as antiatherogenic lipoprotein, consists of heterogeneous particles in terms of size, density and composition, suggesting differences among HDL subclasses in characteristics and functions. We investigated the role of apolipoprotein E (apoE)-containing HDL, a minor HDL subclass, in the cholesterol efflux capacity (CEC) of HDL, which is its predominant atheroprotective function. The CEC of apoE-containing HDL was similar to that of apoE-deficient HDL, but the former exhibited a greater rate increase (1.48-fold) compared to that of the latter (1.10-fold) by the stimulation of THP-1 macrophages with the Liver X Receptor (LXR) agonist. No difference in CEC was observed without the LXR agonist between apoA-I, the main apolipoprotein in HDL, and apoE, whereas the increase in CEC in response to treatment with the LXR agonist was greater for apoA-I (4.25-fold) than for apoE (2.22-fold). Furthermore, the increase in the CEC of apoE-containing HDL induced by the LXR agonist was significantly reduced by treatment with glyburide, an inhibitor of ATP-binding cassette transporter A1 (ABCA1). These results suggest that apoE-containing HDL, unlike apoE-deficient HDL, is involved in cholesterol efflux via ABCA1.

A convex 3D deconvolution algorithm for low photon count fluorescence imaging.

Deconvolution is widely used to improve the contrast and clarity of a 3D focal stack collected using a fluorescence microscope. But despite being extensively studied, deconvolution algorithms can introduce reconstruction artifacts when their underlying noise models or priors are violated, such as when imaging biological specimens at extremely low light levels. In this paper we propose a deconvolution method specifically designed for 3D fluorescence imaging of biological samples in the low-light regime. Our method utilizes a mixed Poisson-Gaussian model of photon shot noise and camera read noise, which are both present in low light imaging. We formulate a convex loss function and solve the resulting optimization problem using the alternating direction method of multipliers algorithm. Among several possible regularization strategies, we show that a Hessian-based regularizer is most effective for describing locally smooth features present in biological specimens. Our algorithm also estimates noise parameters on-the-fly, thereby eliminating a manual calibration step required by most deconvolution software. We demonstrate our algorithm on simulated images and experimentally-captured images with peak intensities of tens of photoelectrons per voxel. We also demonstrate its performance for live cell imaging, showing its applicability as a tool for biological research.

Attenuation-corrected fluorescence spectra unmixing for spectroscopy and microscopy.

In fluorescence measurements, light is often absorbed and scattered by a sample both for excitation and emission, resulting in the measured spectra to be distorted. Conventional linear unmixing methods computationally separate overlapping spectra but do not account for these effects. We propose a new algorithm for fluorescence unmixing that accounts for the attenuation-related distortion effect on fluorescence spectra. Using a matrix representation, we derive forward measurement formation and a corresponding inverse method; the unmixing algorithm is based on nonnegative matrix factorization. We also demonstrate how this method can be extended to a higher-dimensional tensor form, which is useful for unmixing overlapping spectra observed under the attenuation effect in spectral imaging microscopy. We evaluate the proposed methods in simulation and experiments and show that it outperforms a conventional, linear unmixing method when absorption and scattering contributes to the measured signals, as in deep tissue imaging.

Integumental reddish-violet coloration owing to novel dichromatic chromatophores in the teleost fish, Pseudochromis diadema.

In the reddish-violet parts of the skin of the diadema pseudochromis Pseudochromis diadema, we found novel dichromatic chromatophores with a reddish pigment and reflecting platelets. We named these novel cells 'erythro-iridophores'. In standard physiological solution, erythro-iridophores displayed two hues, red and dark violet when viewed with an optical microscope under ordinary transmission light and epi-illumination optics, respectively. Under transmission electron microscopy, however, we observed no typical red chromatosomes, i.e., erythrosomes, in the cytoplasm. High-performance thin-layer chromatography (HPTLC) analysis of the pigment eluted from the erythro-iridophores indicated that carotenoid is the main pigment generating the reddish color. Furthermore, when the irrigating medium was a K(+)-rich saline solution, the color reflected from the erythro-iridophores changed from dark violet to sky blue, but the red coloration remained. The motile activities of the erythro-iridophores may participate in the changes in the reddish-violet shades of the pseudochromis fish.