Design and Validation of a Tool for Neurite Tracing and Analysis in Fluorescence Microscopy Images

Background: For the investigation of the molecular mechanisms involved in neurite outgrowth and differentiation, accurate and reproducible segmentation and quantification of neuronal processes are a prerequisite. To facilitate this task, we developed a semiautomatic neurite tracing technique. This article describes the design and validation of the technique. Methods: The technique was compared to fully manual delineation. Four observers repeatedly traced selected neurites in 20 fluorescence microscopy images of cells in culture, using both methods. Accuracy and reproducibility were determined by comparing the tracings to high-resolution reference tracings, using two error measures. Labor intensiveness was measured in numbers of mouse clicks required. The significance of the results was determined by a Student t-test and by analysis of variance. Results: Both methods slightly underestimated the true neurite length, but the differences were not unanimously significant. The average deviation from the true neurite centerline was a factor 2.6 smaller with the developed technique compared to fully manual tracing. Intraobserver variability in the respective measures was reduced by a factor 6.0 and 23.2. Interobserver variability was reduced by a factor 2.4 and 8.8, respectively, and labor intensiveness by a factor 3.3. Conclusions: Providing similar accuracy in measuring neurite length, significantly improved accuracy in neurite centerline extraction, and significantly improved reproducibility and reduced labor intensiveness, the developed technique may replace fully manual tracing methods

Image informatics strategies for deciphering neuronal network connectivity

Brain function relies on an intricate network of highly dynamic neuronal connections that rewires dramatically under the impulse of various external cues and pathological conditions. Among the neuronal structures that show morphologi- cal plasticity are neurites, synapses, dendritic spines and even nuclei. This structural remodelling is directly connected with functional changes such as intercellular com- munication and the associated calcium-bursting behaviour. In vitro cultured neu- ronal networks are valuable models for studying these morpho-functional changes. Owing to the automation and standardisation of both image acquisition and image analysis, it has become possible to extract statistically relevant readout from such networks. Here, we focus on the current state-of-the-art in image informatics that enables quantitative microscopic interrogation of neuronal networks. We describe the major correlates of neuronal connectivity and present workflows for analysing them. Finally, we provide an outlook on the challenges that remain to be addressed, and discuss how imaging algorithms can be extended beyond in vitro imaging studies

Asymptotic statistics of the n-sided planar Poisson-Voronoi cell. I. Exact results

We achieve a detailed understanding of the $n$-sided planar Poisson-Voronoi cell in the limit of large $n$. Let ${p}\_n$ be the probability for a cell to have $n$ sides. We construct the asymptotic expansion of $\log {p}\_n$ up to terms that vanish as $n\to\infty$. We obtain the statistics of the lengths of the perimeter segments and of the angles between adjoining segments: to leading order as $n\to\infty$, and after appropriate scaling, these become independent random variables whose laws we determine; and to next order in $1/n$ they have nontrivial long range correlations whose expressions we provide. The $n$-sided cell tends towards a circle of radius (n/4\pi\lambda)^{\half}, where $\lambda$ is the cell density; hence Lewis' law for the average area $A\_n$ of the $n$-sided cell behaves as $A\_n \simeq cn/\lambda$ with $c=1/4$. For $n\to\infty$ the cell perimeter, expressed as a function $R(\phi)$ of the polar angle $\phi$, satisfies $d^2 R/d\phi^2 = F(\phi)$, where $F$ is known Gaussian noise; we deduce from it the probability law for the perimeter's long wavelength deviations from circularity. Many other quantities related to the asymptotic cell shape become accessible to calculation.Comment: 54 pages, 3 figure

Prospective cohort study comparing a triceps-sparing and triceps-detaching approach in total elbow arthroplasty:a protocol

BACKGROUND: New surgical approaches have been developed to optimise elbow function after total elbow arthroplasty (TEA). Currently, there is no consensus on the best surgical approach. This study aims to investigate the functional outcomes, prosthetic component position and complication rates after a triceps-sparing and a triceps-detaching approach in TEA. METHODS AND ANALYSIS: A multicentre prospective comparative cohort study will be conducted. All patients with an indication for primary TEA will enrol in either the triceps-sparing or the triceps-detaching cohort. Primary outcome measure is elbow function, specified as fixed flexion deformity. Secondary outcome parameters are self-reported and objectively measured physical functioning, including triceps force, prosthetic component position in standard radiographs and complications. DISCUSSION: The successful completion of this study will clarify which surgical approach yields better functional outcomes, better prosthetic component position and lower complication rates in patients with a TEA. ETHICS AND DISSEMINATION: The Medical Ethics Review Board of University Medical Center Groningen reviewed the study and concluded that it is not clinical research with human subjects as meant in the Medical Research Involving Human Subjects Act (WMO), therefore WMO approval is not needed (METc2019/544). TRIAL REGISTRATION NUMBER: NTR NL8488

Tensor field interpolation with PDEs

We present a unified framework for interpolation and regularisation of scalar- and tensor-valued images. This framework is based on elliptic partial differential equations (PDEs) and allows rotationally invariant models. Since it does not require a regular grid, it can also be used for tensor-valued scattered data interpolation and for tensor field inpainting. By choosing suitable differential operators, interpolation methods using radial basis functions are covered. Our experiments show that a novel interpolation technique based on anisotropic diffusion with a diffusion tensor should be favoured: It outperforms interpolants with radial basis functions, it allows discontinuity-preserving interpolation with no additional oscillations, and it respects positive semidefiniteness of the input tensor data

Spatial Distribution of Cryptic Species Diversity in European Freshwater Amphipods (Gammarus fossarum) as Revealed by Pyrosequencing

In order to understand and protect ecosystems, local gene pools need to be evaluated with respect to their uniqueness. Cryptic species present a challenge in this context because their presence, if unrecognized, may lead to serious misjudgement of the distribution of evolutionarily distinct genetic entities. In this study, we describe the current geographical distribution of cryptic species of the ecologically important stream amphipod Gammarus fossarum (types A, B and C). We use a novel pyrosequencing assay for molecular species identification and survey 62 populations in Switzerland, plus several populations in Germany and eastern France. In addition, we compile data from previous publications (mainly Germany). A clear transition is observed from type A in the east (Danube and Po drainages) to types B and, more rarely, C in the west (Meuse, Rhone, and four smaller French river systems). Within the Rhine drainage, the cryptic species meet in a contact zone which spans the entire G. fossarum distribution range from north to south. This large-scale geographical sorting indicates that types A and B persisted in separate refugia during Pleistocene glaciations. Within the contact zone, the species rarely co-occur at the same site, suggesting that ecological processes may preclude long-term coexistence. The clear phylogeographical signal observed in this study implies that, in many parts of Europe, only one of the cryptic species is present

Studying strategies and types of players:Experiments, logics and cognitive models

How do people reason about their opponent in turn-taking games? Often, people do not make the decisions that game theory would prescribe. We present a logic that can play a key role in understanding how people make their decisions, by delineating all plausible reasoning strategies in a systematic manner. This in turn makes it possible to construct a corresponding set of computational models in a cognitive architecture. These models can be run and fitted to the participants’ data in terms of decisions, response times, and answers to questions. We validate these claims on the basis of an earlier game-theoretic experiment about the turn-taking game “Marble Drop with Surprising Opponent”, in which the opponent often starts with a seemingly irrational move. We explore two ways of segregating the participants into reasonable “player types”. The first way is based on latent class analysis, which divides the players into three classes according to their first decisions in the game: Random players, Learners, and Expected players, who make decisions consistent with forward induction. The second way is based on participants’ answers to a question about their opponent, classified according to levels of theory of mind: zero-order, first-order and second-order. It turns out that increasing levels of decisions and theory of mind both correspond to increasing success as measured by monetary awards and increasing decision times. Next, we use the logical language to express different kinds of strategies that people apply when reasoning about their opponent and making decisions in turn-taking games, as well as the ‘reasoning types’ reflected in their behavior. Then, we translate the logical formulas into computational cognitive models in the PRIMs architecture. Finally, we run two of the resulting models, corresponding to the strategy of only being interested in one’s own payoff and to the myopic strategy, in which one can only look ahead to a limited number of nodes. It turns out that the participant data fit to the own-payoff strategy, not the myopic one. The article closes the circle from experiments via logic and cognitive modelling back to predictions about new experiments

An objective comparison of cell-tracking algorithms

We present a combined report on the results of three editions of the Cell Tracking Challenge, an ongoing initiative aimed at promoting the development and objective evaluation of cell segmentation and tracking algorithms. With 21 participating algorithms and a data repository consisting of 13 data sets from various microscopy modalities, the challenge displays today's state-of-the-art methodology in the field. We analyzed the challenge results using performance measures for segmentation and tracking that rank all participating methods. We also analyzed the performance of all of the algorithms in terms of biological measures and practical usability. Although some methods scored high in all technical aspects, none obtained fully correct solutions. We found that methods that either take prior information into account using learning strategies or analyze cells in a global spatiotemporal video context performed better than other methods under the segmentation and tracking scenarios included in the challenge

Height and timing of growth spurt during puberty in young people living with vertically acquired HIV in Europe and Thailand.

OBJECTIVE: The aim of this study was to describe growth during puberty in young people with vertically acquired HIV. DESIGN: Pooled data from 12 paediatric HIV cohorts in Europe and Thailand. METHODS: One thousand and ninety-four children initiating a nonnucleoside reverse transcriptase inhibitor or boosted protease inhibitor based regimen aged 1-10 years were included. Super Imposition by Translation And Rotation (SITAR) models described growth from age 8 years using three parameters (average height, timing and shape of the growth spurt), dependent on age and height-for-age z-score (HAZ) (WHO references) at antiretroviral therapy (ART) initiation. Multivariate regression explored characteristics associated with these three parameters. RESULTS: At ART initiation, median age and HAZ was 6.4 [interquartile range (IQR): 2.8, 9.0] years and -1.2 (IQR: -2.3 to -0.2), respectively. Median follow-up was 9.1 (IQR: 6.9, 11.4) years. In girls, older age and lower HAZ at ART initiation were independently associated with a growth spurt which occurred 0.41 (95% confidence interval 0.20-0.62) years later in children starting ART age 6 to 10 years compared with 1 to 2 years and 1.50 (1.21-1.78) years later in those starting with HAZ less than -3 compared with HAZ at least -1. Later growth spurts in girls resulted in continued height growth into later adolescence. In boys starting ART with HAZ less than -1, growth spurts were later in children starting ART in the oldest age group, but for HAZ at least -1, there was no association with age. Girls and boys who initiated ART with HAZ at least -1 maintained a similar height to the WHO reference mean. CONCLUSION: Stunting at ART initiation was associated with later growth spurts in girls. Children with HAZ at least -1 at ART initiation grew in height at the level expected in HIV negative children of a comparable age

Pre-launch calibration results of the TROPOMI payload on-board the Sentinel-5 Precursor satellite

The Sentinel-5 Precursor satellite was successfully launched on 13 October 2017, carrying the Tropospheric Monitoring Instrument (TROPOMI) as its single payload. TROPOMI is the next-generation atmospheric sounding instrument, continuing the successes of GOME, SCIAMACHY, OMI, and OMPS, with higher spatial resolution, improved sensitivity, and extended wavelength range. The instrument contains four spectrometers, divided over two modules sharing a common telescope, measuring the ultraviolet, visible, near-infrared, and shortwave infrared reflectance of the Earth. The imaging system enables daily global coverage using a push-broom configuration, with a spatial resolution as low as 7×3.5&thinsp;km2 in nadir from a Sun-synchronous orbit at 824&thinsp;km and an Equator crossing time of 13:30 local solar time. This article reports the pre-launch calibration status of the TROPOMI payload as derived from the on-ground calibration effort. Stringent requirements are imposed on the quality of on-ground calibration in order to match the high sensitivity of the instrument. A new methodology has been employed during the analysis of the obtained calibration measurements to ensure the consistency and validity of the calibration. This was achieved by using the production-grade Level 0 to 1b data processor in a closed-loop validation set-up. Using this approach the consistency between the calibration and the L1b product, as well as confidence in the obtained calibration result, could be established. This article introduces this novel calibration approach and describes all relevant calibrated instrument properties as they were derived before launch of the mission. For most of the relevant properties compliance with the calibration requirements could be established, including the knowledge of the instrument spectral and spatial response functions. Partial compliance was established for the straylight correction; especially the out-of-spectral-band correction for the near-infrared channel needs future validation. The absolute radiometric calibration of the radiance and irradiance responsivity is compliant with the high-level mission requirements, but not with the stricter calibration requirements as the available on-ground validation shows. The relative radiometric calibration of the Sun port was non-compliant. The non-compliant subjects will be addressed during the in-flight commissioning phase in the first 6 months following launch.</p