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.

Laser writing of nonlinear optical properties in silver-doped phosphate glass

The formation of both local second- and third-harmonic generations (SHG and THG) induced by a train of femtosecond laser pulses in silver-doped phosphate glasses is addressed. Based on modeling calculations, including various diffusion and kinetic processes, THG is shown to result from the formation of silver clusters. The latter organize into a ring-shape structure, leading to the emergence of a static electric field. By breaking the glass centro-symmetry, this field gives rise to a local effective second-order susceptibility, inducing SHG. Both theoretically predicted SHG and THG evolutions with respect to the number of pulses in the train are in good agreement with experimental observations. In particular, the observed reaching of a maximum in the nonlinear optical responses after a few thousands of pulses is explained by the competition of various physical processes. A cooling of the glass is shown to improve the process efficiency of the laser writing of second-order nonlinearity.

Dual-color control and inhibition of direct laser writing in silver-containing phosphate glasses

We report on dual-color control of femtosecond direct laser writing (DLW) in a noncommercial silver-containing zinc phosphate glass, thanks to an additional illumination with a cw (continuous wave) UV laser, either after the femtosecond irradiation or simultaneously. By tuning the cw UV power, we demonstrate the tunable control and inhibition of the production efficiency of laser-induced fluorescent silver clusters, leading up to 100% inhibition for simultaneous co-illumination when the laser writing is performed close enough to the permanent structuring threshold. The role of the cw UV illumination is discussed in terms of inhibition of the silver cluster precursors or of dissolution of the laser-induced silver clusters. These results show the ability of laser writing inhibition in our photosensitive silver-containing phosphate glass, which is a necessary step to further develop super-resolution laser writing approaches, such as STED-like DLW, either of fluorescent silver clusters or of silver metallic nanoparticles with plasmonic properties.

Patterning linear and nonlinear optical properties of photosensitive glasses by femtosecond structured light

We report on structured light-induced femtosecond direct laser writing (DLW) under tight focusing in non-commercial silver-containing zinc phosphate glass, which leads to original patterns of fluorescent silver clusters. These fluorescence topologies show unique features of frustrated diffusion of charged species, giving rise to distorted silver cluster spatial distributions. Fluorescence and second harmonic generation correlative microscopy demonstrate the realization of structured light-induced direct laser poling, resulting from a laser-induced permanent and stable electric field buried inside the modified glass. Thus, structured light-induced DLW remarkably enables both linear and nonlinear patterning. This work highlights the interest of optical phase engineering to obtain nontrivial beam profiles and subsequent photo-induced patterns that cannot be reached under Gaussian beam irradiation.

Two-photon excited fluorescence in the LYB:Eu monoclinic crystal: towards a new scheme of single-beam dual-voxel direct laser writing in crystals

We report on two-photon excited fluorescence in the oriented Eu(3+)doped LYB monoclinic crystal under femtosecond laser tight focusing. Due to spatial walk-off, the two polarization modes of the incident femtosecond beam simultaneously provide the independent excitation of two distinct focuses, leading to a single-beam dual-voxel nonlinear excitation of fluorescence below material modification threshold. These observations emphasize on the anisotropy of both two-photon absorption as well as fluorescence emission. They demonstrate the localized control of the nonlinear energy deposit, thanks to the adjustment of both the input power and polarization, by properly balancing the injected energy in each voxel. Such approach should be considered for future direct laser writing of waveguides in propagation directions out of the dielectric axes, so as to optimally cope with the highly probable anisotropy of laser-induced material modification thresholds in these crystals. These results open new ways for further potential developments in direct laser writing as the simultaneous inscription of double-line structures for original waveguides processes.

Three-dimensional direct femtosecond laser writing of second-order nonlinearities in glass

We demonstrate that direct femtosecond laser writing in silver-containing zinc and gallium phosphate glass enables generation of three-dimensional (3D) optical second-order nonlinear microstructures having an χ(2) value about 2.5 times that of quartz. The proposed physical model involves photo-reduction, photo-dissociation, and migration of silver species within the glass matrix. 3D laser-written second-order nonlinear structures could become a new class of nonlinear optical components.

Beat the diffraction limit in 3D direct laser writing in photosensitive glass

Three-dimensional (3D) femtosecond laser direct structuring in transparent materials is widely used for photonic applications. However, the structure size is limited by the optical diffraction. Here we report on a direct laser writing technique that produces subwavelength nanostructures independently of the experimental limiting factors. We demonstrate 3D nanostructures of arbitrary patterns with feature sizes down to 80 nm, less than one tenth of the laser processing wavelength. Its ease of implementation for novel nanostructuring, with its accompanying high precision will open new opportunities for the fabrication of nanostructures for plasmonic and photonic devices and for applications in metamaterials.

Three-dimensional optical data storage using third-harmonic generation in silver zinc phosphate glass

We demonstrate the possibility of three-dimensional optical data storage inside a specific zinc phosphate glass containing silver by using third-harmonic generation (THG) imaging. Information is stored inside the glass with femtosecond laser irradiation below the refractive index modification threshold. We use the same laser for THG readout. The capability of storage with this technique is discussed.