arXiv subjects

Orestis Faklaris

Publications and source records attributed to Orestis Faklaris.

7 recordsLinked to original sources

arXiv2025

Harmonizing the Generation and Pre-publication Stewardship of FAIR Image Data

Alongside molecular insights into genes and proteins, biological imaging holds great promise for deepening scientific understanding of complex cellular systems and advancing predictive, personalized therapies for human health. To realize this potential, quality-assured image data must be shared globally across laboratories to enable comparison, pooling, and reanalysis-unlocking value far beyond the original purpose of data collection. Two broad sets of requirements are essential to enable image data sharing in the life sciences. The companion article Enabling Global Image Data Sharing in the Life Sciences outlines the need to develop cyberinfrastructure for sharing bioimage data. In this manuscript, we detail a broad set of requirements, which involves collecting, managing, presenting, and propagating contextual information essential to assess the quality, understand the content, interpret the scientific implications, and reuse bioimage data in the context of the experimental details. We start by providing an overview of the main lessons learned to date through international community activities, which have recently made considerable progress toward generating community standard practices for imaging Quality Control (QC) and metadata. We then provide a clear set of recommendations for amplifying this work. The driving goal is to address remaining challenges and democratize access to everyday practices and tools for a spectrum of biomedical researchers, regardless of their expertise, access to resources, and geographical location.

q-bio.OT↗

arXiv2021

A perspective on Microscopy Metadata: data provenance and quality control

The application of microscopy in biomedical research has come a long way since Antonie van Leeuwenhoek discovered unicellular organisms. Countless innovations have positioned light microscopy as a cornerstone of modern biology and a method of choice for connecting omics datasets to their biological and clinical correlates. Still, regardless of how convincing published imaging data looks, it does not always convey meaningful information about the conditions in which it was acquired, processed, and analyzed. Adequate record-keeping, reporting, and quality control are therefore essential to ensure experimental rigor and data fidelity, allow experiments to be reproducibly repeated, and promote the proper evaluation, interpretation, comparison, and re-use. To this end, microscopy images should be accompanied by complete descriptions detailing experimental procedures, biological samples, microscope hardware specifications, image acquisition parameters, and image analysis procedures, as well as metrics accounting for instrument performance and calibration. However, universal, community-accepted Microscopy Metadata standards and reporting specifications that would result in Findable Accessible Interoperable and Reproducible (FAIR) microscopy data have not yet been established. To understand this shortcoming and to propose a way forward, here we provide an overview of the nature of microscopy metadata and its importance for fostering data quality, reproducibility, scientific rigor, and sharing value in light microscopy. The proposal for tiered Microscopy Metadata Specifications that extend the OME Data Model put forth by the 4D Nucleome Initiative and by Bioimaging North America [1-3] as well as a suite of three complementary and interoperable tools are being developed to facilitate the process of image data documentation and are presented in related manuscripts [4-6].

q-bio.QM↗

arXiv2021

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

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.

q-bio.OT↗

arXiv2020

Interpretation of Confocal ISO 21073: 2019 confocal microscopes: Optical data of fluorescence confocal microscopes for biological imaging- Recommended Methodology for Quality Control

The performance of a confocal imaging system may be no better than a general-purpose widefield system if it is not properly maintained or quality controlled. The publication of ISO 21073, 'Confocal microscopes- Optical data of fluorescence confocal microscopes for biological imaging', set a standard for the minimal Quality Control (QC) that should be performed for Confocal Microscopes. Here we describe methodology for performing the QC requirements to satisfy ISO 21073, as well as suggesting other QC methods that should be performed to obtain a minimum level of information about the microscope system.

q-bio.OT↗

arXiv2009

Photoluminescent diamond nanoparticles for cell labeling: study of the uptake mechanism in mammalian cells

Diamond nanoparticles (nanodiamonds) have been recently proposed as new labels for cellular imaging. For small nanodiamonds (size <40 nm) resonant laser scattering and Raman scattering cross-sections are too small to allow single nanoparticle observation. Nanodiamonds can however be rendered photoluminescent with a perfect photostability at room temperature. Such a remarkable property allows easier single-particle tracking over long time-scales. In this work we use photoluminescent nanodiamonds of size <50 nm for intracellular labeling and investigate the mechanism of their uptake by living cells . By blocking selectively different uptake processes we show that nanodiamonds enter cells mainly by endocytosis and converging data indicate that it is clathrin mediated. We also examine nanodiamonds intracellular localization in endocytic vesicles using immunofluorescence and transmission electron microscopy. We find a high degree of colocalization between vesicles and the biggest nanoparticles or aggregates, while the smallest particles appear free in the cytosol. Our results pave the way for the use of photoluminescent nanodiamonds in targeted intracellular labeling or biomolecule delivery

physics.optics↗

arXiv2009

Comparison of the photoluminescence properties of semiconductor quantum dots and non-blinking diamond nanoparticles. Observation of the diffusion of diamond nanoparticles in living cells

Long-term observations of photoluminescence at the single-molecule level were until recently very diffcult, due to the photobleaching of organic ?uorophore molecules. Although inorganic semiconductor nanocrystals can overcome this diffculty showing very low photobleaching yield, they suffer from photoblinking. A new marker has been recently introduced, relying on diamond nanoparticles containing photoluminescent color centers. In this work we compare the photoluminescence of single quantum dots (QDs) to the one of nanodiamonds containing a single-color center. Contrary to other markers, photoluminescent nanodiamonds present a perfect photostability and no photoblinking. At saturation of their excitation, nanodiamonds photoluminescence intensity is only three times smaller than the one of QDs. Moreover, the bright and stable photoluminescence of nanodiamonds allows wide field observations of single nanoparticles motion. We demonstrate the possibility of recording the tra jectory of such single particle in culture cells.

physics.optics↗

arXiv2007

25-nm diamond crystals hosting single NV color centers sorted by photon-correlation near-field microscopy

Diamond nanocrystals containing highly photoluminescent color centers are attractive non-classical and near-field light sources. For near-field applications the size of the nanocrystal is crucial since it defines the optical resolution. NV (Nitrogen-Vacancy) color centers are efficiently created by proton irradiation and annealing of a nanodiamond powder. Using near-field microscopy and photon statistics measurements, we show that nanodiamond with size down to 25 nm can hold a single NV color center with bright and stable photoluminescence.

cond-mat.mtrl-sci↗