Publisher Correction: DeepSTORM3D: dense 3D localization microscopy and PSF design by deep learning.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

DeepSTORM3D: dense 3D localization microscopy and PSF design by deep learning.

An outstanding challenge in single-molecule localization microscopy is the accurate and precise localization of individual point emitters in three dimensions in densely labeled samples. One established approach for three-dimensional single-molecule localization is point-spread-function (PSF) engineering, in which the PSF is engineered to vary distinctively with emitter depth using additional optical elements. However, images of dense emitters, which are desirable for improving temporal resolution, pose a challenge for algorithmic localization of engineered PSFs, due to lateral overlap of the emitter PSFs. Here we train a neural network to localize multiple emitters with densely overlapping Tetrapod PSFs over a large axial range. We then use the network to design the optimal PSF for the multi-emitter case. We demonstrate our approach experimentally with super-resolution reconstructions of mitochondria and volumetric imaging of fluorescently labeled telomeres in cells. Our approach, DeepSTORM3D, enables the study of biological processes in whole cells at timescales that are rarely explored in localization microscopy.

High BMI and the risk for incident type 1 Diabetes Mellitus: a systematic review and meta-analysis of aggregated cohort studies.

BACKGROUND: There is uncertainty regarding the role of obesity in type 1 diabetes development. The aim of this systematic review and meta-analysis was to collect and synthesize evidence regarding BMI and the risk of developing type 1 diabetes. METHODS: A systematic review and meta-analysis were conducted to assess the association between BMI and incident type 1 diabetes. Databases were searched up to June 2022. Cohort studies were included reporting the association between overweight and/or obesity, as measured by BMI after age 2 years, with incident type 1 diabetes. Independent reviewers extracted data and assessed study quality. Risk estimates were pooled using a random-effects model. RESULTS: Ten cohort studies met the inclusion criteria. The seven studies that classified BMI into categories were of high quality and involved 1,690,660 individuals and 1979 incident type 1 diabetes cases. The pooled risk ratio (RR) for type 1 diabetes was 1.35 (95% CI 0.93-1.97) among people with overweight (3 studies); 2.17 (95% CI 1.75-2.69) among people with obesity (5 studies); and 1·87 (95% CI 1.52-2.29) among people with overweight/obesity (two studies merged the categories). These point estimates persisted in sensitivity analyses that addressed the duration of follow-up, variability in baseline risk for incident type 1 diabetes, and potential misclassifications related to exposure or outcome definitions. People with overweight/obesity had a 2.55 (95% CI 1.11-5.86) greater risk for incident type 1 diabetes with positive islet autoantibodies. CONCLUSION: This systematic review and meta-analysis of high-quality observational cohort studies indicated an association between high BMI and the risk of type 1 diabetes, in a graded manner.

Multicolor localization microscopy and point-spread-function engineering by deep learning.

Deep learning has become an extremely effective tool for image classification and image restoration problems. Here, we apply deep learning to microscopy and demonstrate how neural networks can exploit the chromatic dependence of the point-spread function to classify the colors of single emitters imaged on a grayscale camera. While existing localization microscopy methods for spectral classification require additional optical elements in the emission path, e.g., spectral filters, prisms, or phase masks, our neural net correctly identifies static and mobile emitters with high efficiency using a standard, unmodified single-channel configuration. Furthermore, we show how deep learning can be used to design new phase-modulating elements that, when implemented into the imaging path, result in further improved color differentiation between species, including simultaneously differentiating four species in a single image.

Characterizing different cognitive and neurobiological profiles in a community sample of children using a non-parametric approach: An fMRI study.

Executive Functions (EF) is an umbrella term for a set of mental processes geared towards goal-directed behavior supporting academic skills such as reading abilities. One of the brain's functional networks implicated in EF is the Default Mode Network (DMN). The current study uses measures of inhibitory control, a main sub-function of EF, to create cognitive and neurobiological "inhibitory control profiles" and relate them to reading abilities in a large sample (N = 5055) of adolescents aged 9-10 from the Adolescent Brain Cognitive Development (ABCD) study. Using a Latent Profile Analysis (LPA) approach, data related to inhibitory control was divided into four inhibition classes. For each class, functional connectivity within the DMN was calculated from resting-state data, using a non-parametric algorithm for detecting group similarities. These inhibitory control profiles were then related to reading abilities. The four inhibitory control groups showed significantly different reading abilities, with neurobiologically different DMN segregation profiles for each class versus controls. The current study demonstrates that a community sample of children is not entirely homogeneous and is composed of different subgroups that can be differentiated both behaviorally/cognitively and neurobiologically, by focusing on inhibitory control and the DMN. Educational implications relating these results to reading abilities are noted.

Learning Optimal Wavefront Shaping for Multi-Channel Imaging.

Fast acquisition of depth information is crucial for accurate 3D tracking of moving objects. Snapshot depth sensing can be achieved by wavefront coding, in which the point-spread function (PSF) is engineered to vary distinctively with scene depth by altering the detection optics. In low-light applications, such as 3D localization microscopy, the prevailing approach is to condense signal photons into a single imaging channel with phase-only wavefront modulation to achieve a high pixel-wise signal to noise ratio. Here we show that this paradigm is generally suboptimal and can be significantly improved upon by employing multi-channel wavefront coding, even in low-light applications. We demonstrate our multi-channel optimization scheme on 3D localization microscopy in densely labelled live cells where detectability is limited by overlap of modulated PSFs. At extreme densities, we show that a split-signal system, with end-to-end learned phase masks, doubles the detection rate and reaches improved precision compared to the current state-of-the-art, single-channel design. We implement our method using a bifurcated optical system, experimentally validating our approach by snapshot volumetric imaging and 3D tracking of fluorescently labelled subcellular elements in dense environments.

Hypoxia causes connexin 43 internalization in neonatal rat ventricular myocytes.

Gap junctions produce low resistance pathways between cardiomyocytes and are major determinants of electrical conduction in the heart. Altered distribution and function of connexin 43 (Cx43), the major gap junctional protein in the ventricles, can slow conduction, and thus contribute to arrhythmogenesis in experimental models such as ischemic rat heart and pacing-induced atrial fibrillation. The mechanisms underlying reduced gap junctional density and conductance during ischemia may involve decreased Cx43 synthesis, increased degradation and/or Cx43 migration into areas which do not contribute to intercellular communication. To test more rigorously the hypothesis that hypoxia resulting from ischemia causes Cx43 internalization, we infected neonatal rat ventricular myocytes (NRVM) with a Cx43-GFP chimera, which enabled us to investigate by means of confocal microscopy the effect of hypoxia (1% O2 for 5 h) on Cx43 distribution in live cardiomyocytes. Importantly, this protocol permitted each culture to serve as its own control. To this end we used life confocal microscopy analysis to determine in the same pair of myocytes the effects of hypoxia on Cx43-GFP distribution at the gap junctional (GJ) and non-GJ areas. In support of this hypothesis, we found that compared to normoxia, 5 h of hypoxia reduced the Cx43-GFP signal at the GJ areas (defined as the border area) and caused a corresponding increase in the Cx43-GFP signal at the non-border areas, thus providing an additional explanation for the intercellular uncoupling during ischemic conditions.