QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy

A modern day light microscope has evolved from a tool devoted to making primarily empirical observations to what is now a sophisticated , quantitative device that is an integral part of both physical and life science research. Nowadays, microscopes are found in nearly every experimental laboratory. However, despite their prevalent use in capturing and quantifying scientific phenomena, neither a thorough understanding of the principles underlying quantitative imaging techniques nor appropriate knowledge of how to calibrate, operate and maintain microscopes can be taken for granted. This is clearly demonstrated by the well-documented and widespread difficulties that are routinely encountered in evaluating acquired data and reproducing scientific experiments. Indeed, studies have shown that more than 70% of researchers have tried and failed to repeat another scientist's experiments, while more than half have even failed to reproduce their own experiments. One factor behind the reproducibility crisis of experiments published in scientific journals is the frequent underreporting of imaging methods caused by a lack of awareness and/or a lack of knowledge of the applied technique. Whereas quality control procedures for some methods used in biomedical research, such as genomics (e.g. DNA sequencing, RNA-seq) or cytometry, have been introduced (e.g. ENCODE), this issue has not been tackled for optical microscopy instrumentation and images. Although many calibration standards and protocols have been published, there is a lack of awareness and agreement on common standards and guidelines for quality assessment and reproducibility. In April 2020, the QUality Assessment and REProducibility for instruments and images in Light Microscopy (QUAREP-LiMi) initiative was formed. This initiative comprises imaging scientists from academia and industry who share a common interest in achieving a better understanding of the performance and limitations of microscopes and improved quality control (QC) in light microscopy. The ultimate goal of the QUAREP-LiMi initiative is to establish a set of common QC standards, guidelines, metadata models and tools, including detailed protocols, with the ultimate aim of improving reproducible advances in scientific research. This White Paper (1) summarizes the major obstacles identified in the field that motivated the launch of the QUAREP-LiMi initiative; (2) identifies the urgent need to address these obstacles in a grassroots manner, through a community of stakeholders including, researchers, imaging scientists, bioimage analysts, bioimage informatics developers, corporate partners, funding agencies, standards organizations, scientific publishers and observers of such; (3) outlines the current actions of the QUAREP-LiMi initiative and (4) proposes future steps that can be taken to improve the dissemination and acceptance of the proposed guidelines to manage QC. To summarize, the principal goal of the QUAREP-LiMi initiative is to improve the overall quality and reproducibility of light microscope image data by introducing broadly accepted standard practices and accurately captured image data metrics.

Spinning pupil aberration measurement for anisoplanatic deconvolution

The aberrations in an optical microscope are commonly measured and corrected at one location in the field of view, within the so-called isoplanatic patch. Full-field correction is desirable for high-resolution imaging of large specimens. Here we present, to the best of our knowledge, a novel wavefront detector, based on pupil sampling with subapertures, measuring the aberrated wavefront phase at each position of the specimen. Based on this measurement, we propose a region-wise deconvolution that provides an anisoplanatic reconstruction of the sample image. Our results indicate that the measurement and correction of the aberrations can be performed in a wide-field fluorescence microscope over its entire field of view.

Gravitational Decoherence and the Possibility of Its Interferometric Detection

We present a general master equation describing the quantum dynamics of a scalar bosonic field interacting with an external weak and stochastic gravitational field. The dynamics predicts decoherence both in position and in energy momentum. We show how the master equation reproduces, thus generalizing, the previous results in the literature by taking appropriate limits. We estimate the effect of gravitational decoherence in atom interferometers, providing also a straightforward way to assess the magnitude of the effect.

Nail changes in children with idiopathic congenital clubfoot deformity

BACKGROUND/OBJECTIVES

Nail alterations are commonly seen in cases of idiopathic clubfoot and may cause parental concern. The nature of and whether these changes are congenital or develop secondary to treatment has been poorly investigated. The aim of this study was to evaluate toenail morphology in clubfoot patients at presentation, to re-evaluate them during the course of treatment for the clubfoot, and to analyze findings in the light of the few literature reports for healthy children of the same age.

METHODS

Thirty infants (21 males and 9 females) with idiopathic clubfoot were prospectively enrolled at the Anna Meyer Children's University Hospital. Nails of affected and non-affected feet were evaluated by a team of pediatric dermatologists at presentation and re-evaluated once per patient during the bracing period of Ponseti treatment.

RESULTS

Toenails of affected (47) and non-affected (13) feet were abnormal at presentation in 43.3% of patients, in both clubfeet (40.4%) and non-affected feet (38.5%), but most changes were physiologic or transitory alterations, commonly found in healthy children, with nail concavity (koilonychia) being the most common finding (29.7%). Changes were not related to clubfoot severity or laterality (P > .05). In most (76.9%) unilateral cases, there was concordance of nail changes between clubfoot and non-affected foot. At re-evaluation (follow-up time 410 ± 207 days), nail problems were more frequent (53.3%); ingrown toenail was the most common (21.6%).

CONCLUSIONS

The presence of nail alterations seems not to be caused by clubfoot pathology and could be related to unfavorable local condition in the brace.

Multispectral compressive fluorescence lifetime imaging microscopy with a SPAD array detector

Multispectral/hyperspectral fluorescence lifetime imaging microscopy (λFLIM) is a promising tool for studying functional and structural biological processes. The rich information content provided by a multidimensional dataset is often in contrast with the acquisition speed. In this work, we develop and experimentally demonstrate a wide-field λFLIM setup, based on a novel time-resolved 18×1 single-photon avalanche diode array detector working in a single-pixel camera scheme, which parallelizes the spectral detection, reducing measurement time. The proposed system, which implements a single-pixel camera with a compressive sensing scheme, represents an optimal microscopy framework towards the design of λFLIM setups.

Automatic imaging of Drosophila embryos with light sheet fluorescence microscopy on chip

We present a microscope on chip for automated imaging of Drosophila embryos by light sheet fluorescence microscopy. This integrated device, constituted by both optical and microfluidic components, allows the automatic acquisition of a 3D stack of images for specimens diluted in a liquid suspension. The device has been fully optimized to address the challenges related to the specimens under investigation. Indeed, the thickness and the high ellipticity of Drosophila embryos can degrade the image quality. In this regard, optical and fluidic optimization has been carried out to implement dual-sided illumination and automatic sample orientation. In addition, we highlight the dual color investigation capabilities of this device, by processing two sample populations encoding different fluorescent proteins. This work was made possible by the versatility of the used fabrication technique, femtosecond laser micromachining, which allows straightforward fabrication of both optical and fluidic components in glass substrates.

The Serum Immunoglobulin E Level: Is There a Relationship With the Clinical Course of the Gianotti-Crosti Syndrome?

Background: Gianotti Crosti syndrome (GCS) is a self-healing condition with a spontaneous resolution in 2-6 weeks but, even if rarely, recurrent episodes have been reported. Objective: The aim of this observational study is to investigate serum Immunoglobulin E (IgE) level in children with GCS, evaluating if there is a relationship between IgE level and clinical course of the disease. Methods: Children with GCS diagnosed at a tertiary care children's university hospital between June 2018 and November 2019 were prospectively enrolled. Demographic, clinical and hematochemical data of children investigated were collected. In particular, IgE level were investigated at symptoms onset and, if available, at the following blood tests. Patients were divided in 2 groups on the bases of the clinical course: children with a chronic relapsing course and children who did not present any relapse. Results: Among 29 patients enrolled in this study, 14 (48.3%) children had a chronic relapsing course and 15 (51.7%) did not present any relapse. A statistically significant difference was present considering the length of the disease: 210 days (IQR: 161.25-255) for patients with a chronic relapsing course compared to 40 days (IQR: 30-75) for the other group (p < 0.0001). About the median IgE level in the 2 groups, a value about 10 time higher was found in children with chronic course compared to the other group (1,144 vs. 116 U/mL) with a statistically significant difference (p < 0.0001). Conclusion: Despite the study limitations, a significant correlation between higher IgE levels and chronic-relapsing course of the GCS can be assumed.

Lichen sclerosus with enlarged vessels: A variant of lichen sclerosus in young girls

Vascular findings have rarely been described in the setting of lichen sclerosus. Enlarged vessels within the atrophic plaques have been observed on the free margins of the labia minora and clitoral hood. The enlarged vessels completely remit upon treatment of lichen sclerosus with an ultra-potent corticosteroid ointment in the acute phase. During maintenance therapy with calcineurin inhibitors, there was no recurrence of the enlarged vessels.

Deconvolved Image Restoration From Auto-Correlations

The recovery of a real signal from its auto-correlation is a wide-spread problem in computational imaging, and it is equivalent to retrieve the phase linked to a given Fourier modulus. Image-deconvolution, on the other hand, is a funda- mental aspect to take into account when we aim at increasing the resolution of blurred signals. These problems are addressed separately in a large number of experimental situations, ranging from adaptive astronomy to optical microscopy. Here, instead, we tackle both at the same time, performing auto-correlation inversion while deconvolving the current object estimation. To this end, we propose a method based on I -divergence optimization, turning our formalism into an iterative scheme inspired by Bayesian-based approaches. We demonstrate the method by recovering sharp signals from blurred auto-correlations, regardless of whether the blurring acts in auto-correlation, object, or Fourier domain.

Bayesian adaptive decision-theoretic designs for multi-arm multi-stage clinical trials

Multi-arm multi-stage clinical trials in which more than two drugs are simultaneously investigated provide gains over separate single- or two-arm trials. In this paper we propose a generic Bayesian adaptive decision-theoretic design for multi-arm multi-stage clinical trials with K (K≥2) arms. The basic idea is that after each stage a decision about continuation of the trial and accrual of patients for an additional stage is made on the basis of the expected reduction in loss. For this purpose, we define a loss function that incorporates the patient accrual costs as well as costs associated with an incorrect decision at the end of the trial. An attractive feature of our loss function is that its estimation is computationally undemanding, also when K > 2. We evaluate the frequentist operating characteristics for settings with a binary outcome and multiple experimental arms. We consider both the situation with and without a control arm. In a simulation study, we show that our design increases the probability of making a correct decision at the end of the trial as compared to nonadaptive designs and adaptive two-stage designs.

A retrospective study on clinical subtypes and management of morphea in 10 Italian Dermatological Units

BACKGROUND

There are still few dermatological studies on morphea. We evaluated the epidemiological and clinical features and management of pediatric morphea, reporting dermatologists experience.

METHODS

A multicenter retrospective observational study was carried out on the epidemiological and clinical features and management of the disease between 01/01/2009 and 01/10/2014 in 10 Italian Dermatological Units.

RESULTS

We collected the data of 69 children affected by: circumscribed morphea (39.1%); linear morphea of trunk and limbs (14.5%); en coupe de sabre morphea (ECDS) (14.5%); progressive facial hemiatrophy (8.7%); generalized form (18.8%); mixed morphea (4.4%). The mean age at onset was 6.86±3.21 years, mainly between 2 and 8 years, but is statistically significantly lower for ECDS (4.5±3.03). Localizations were: head/neck (30.4%), limbs (26.1%), trunk (14.5%), 2 or more sites (29%), most often the trunk plus limbs. Extracutaneous manifestations were observed in 26.1% patients. 10 patients presented a second autoimmune disorder. Treatments were topical in 26.1% cases and systemic (alone or associated with topical treatments) in 68.1%.

CONCLUSIONS

There was a lack of uniformity in the management of patients and an increasing awareness of dermatologists on the use of systemic therapies, in particular of methotrexate, which is no longer exclusive to rheumatologists. Methotrexate causes stabilization and improvement of the clinical signs, but topical creams are still considered adjuvant or maintenance therapies during/after the use of systemic drugs.

Narrowing the Parameter Space of Collapse Models with Ultracold Layered Force Sensors

Despite the unquestionable empirical success of quantum theory, witnessed by the recent uprising of quantum technologies, the debate on how to reconcile the theory with the macroscopic classical world is still open. Spontaneous collapse models are one of the few testable solutions so far proposed. In particular, the continuous spontaneous localization (CSL) model has become subject of intense experimental research. Experiments looking for the universal force noise predicted by CSL in ultrasensitive mechanical resonators have recently set the strongest unambiguous bounds on CSL. Further improving these experiments by direct reduction of mechanical noise is technically challenging. Here, we implement a recently proposed alternative strategy that aims at enhancing the CSL noise by exploiting a multilayer test mass attached on a high quality factor microcantilever. The test mass is specifically designed to enhance the effect of CSL noise at the characteristic length r_{c}=10^{-7}  m. The measurements are in good agreement with pure thermal motion for temperatures down to 100 mK. From the absence of excess noise, we infer a new bound on the collapse rate at the characteristic length r_{c}=10^{-7}  m, which improves over previous mechanical experiments by more than 1 order of magnitude. Our results explicitly challenge a well-motivated region of the CSL parameter space proposed by Adler.