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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 experiments1. 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 technique2,3. 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. ENCODE4), 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 reproducibility5.
In April 2020, the QUality Assessment and REProducibility for instruments and images in Light Microscopy (QUAREP-LiMi) initiative6 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 models7,8, and tools9,10, 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 scientists11, bioimage analysts, bioimage informatics developers, corporate partners, Funding agencies, standards organizations, scientific publishers, and observers of such; 3) outlines the current actions of the QUAREPLiMi 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.
The development of new fluorescent organic probes effective in the NIR-II region is currently a fast-growing field and represents a challenge in the domain of medical imaging. In this study, we have designed and synthesized an innovative series of aza-boron dipyrromethenes emitting in the NIR-II region. We have investigated the effect of different water-solubilizing groups not only on the photophysical properties of the compounds but also on their in vitro and in vivo performance after bioconjugation to the antibody trastuzumab. Remarkably, we discovered that the most lipophilic compound unexpectedly displayed the most favorable in vivo properties after bioconjugation. This underlines the profound influence that the fluorophore functionalization approach can have on the efficiency of the resulting imaging agent.
Im Verbundprojekt RUSEKU wurde die Probenahme von Wasserproben entscheidend weiterentwickelt. Wichtig ist hierbei zu gewährleisten, dass genügend Merkmalsträger in jeder Probe untersucht werden. Es muss daher eine für den Probenahmeort repräsentative Beprobung hinsichtlich des Wasservolumens in Abhängigkeit der Partikelanzahl gewährleistet sein.
Das Hauptaugenmerk lag im vorliegenden Projekt auf einer praxisnahen Beprobungsstrategie. Es wurden verschiedene Konzepte ausprobiert.
• Grundsätzlich hat sich gezeigt, dass eine Stichprobe eine Momentaufnahme des MP-Massengehaltes zeigt. Es wird eine hohe Statistik, also eine Vielzahl an Messungen am gleichen Probenahmeort, benötigt, um eine valide Aussage über den MP-Gehalt zu machen.
• Es zeigt sich, dass eine integrale Probenahme über mehrere Wochen mit dem SK routinemäßig möglich ist. Die erfassten MP-Massen sind reproduzierbar und robust.
• Die DFZ ist für Stichproben geeignet. Partikel < 50 µm werden eventuell unterschätzt
• Die fraktionierte Filtration kann für Stich- und Mischproben direkt im Feld genutzt werden. Fraktionen von 10 und 5 µm werden später im Labor Vakuum filtriert. Es erfolgt eine Fraktionierung der Probe mit Siebmaschenweiten von 1000, 500, 100, 50, 10 und 5 µm.
• Die fraktionierte Filtration kann auch anschließend an die Beprobung mit dem SK zur Anwendung kommen. Wird die mit dem SK gewonnene Wasserprobe fraktioniert filtriert, kann neben einem MP-Gesamtgehalt auch eine Einschätzung über die Partikelgrößen gewonnen werden.
• Für Wässer mit geringen Partikelzahlen wurde ein Messfiltertiegel entwickelt. Dieser hat eine Maschenweite von 6 µm. Seine Anwendung kann mögliche Verluste beim Transferieren vom Probenahmetool zum Messgefäß und mögliche Kontaminationen reduzieren.
Die Optimierung der Probenahmestrategie wurde durch Modellversuche und Simulationen unterstützt. Modellversuche zum Sinkverhalten und Simulationen von MP in realen Gewässern verdeutlichten das komplexe Verhalten der Partikel. Es konnte gezeigt werden, dass Partikel ab einer bestimmten Größe (und kleiner) bei genügend starker Turbulenz sich in der Wassersäule unabhängig von ihrer Dichte verhalten und so auch MP mit kleiner Dichte (z.B. PE) in der gesamten Wassersäule zu finden sind. Es konnte mit dem TEM die Existenz von NP gezeigt werden.
Ein wesentlicher Aspekt des RUSEKU Projektes war die Beprobung realer Kompartimente. Beprobt wurde neben Oberflächengewässern, das urbane Abwassersystem der Stadt Kaiserslautern, Waschmaschinenabwasser und Flaschenwasser.
• In Oberflächengewässern wurde hauptsächlich PE gefunden. Je nach Probe und Gewässer konnten auch PP, PS, PET, PA, SBR und Acrylate nachgewiesen werden.
• Im urbanen Abwassersystem der Stadt Kaiserslautern konnte an allen Probenahmestandorten MP nachgewiesen werden. Es wurde hauptsächlich PE, neben geringeren Mengen an PP, PS und SBR gefunden. Nach einem Regenereignis war der SBR Anteil deutlich erhöht.
• Die Beprobung eines realen Wäschepostens, bestehend aus T-Shirts und Hemden mit PA/CO oder PES/CO Mischgewebe, zeigte einen PA- und PES-Austrag im Waschwasser. Der überwiegende Teil der detektierten Fasern ist aber auf Baumwolle zurückzuführen. Reine gravimetrische Messungen zur Detektion von MP führen zu einer starken Überschätzung.
• In Flaschenwasser (PET-Flaschen) konnte MP detektiert werden. PET wurde nur im stillen Mineralwasser, nicht in Mineralwasser mit Kohlensäure gefunden werden. Teilweise wurde auch das MP-Material des Verschlusses im Wasser detektiert.
• Für Luftproben konnte ein Aufbau zur größenselektiven Beprobung getestet werden.
Neben der Probenahme hat das Projekt auch gezeigt, dass die TED-GC/MS geeignet für die MP-Detektion im Routinebetrieb ist. Die TED-GC/MS konnte weiter optimiert werden. Es wurden MP-Massen bestimmt.
Im Projekt wurden erste realitätsnahe Referenzmaterialien für die MP Detektion hergestellt. Die Herstellung von realitätsnahen Polymeren in ausreichender Homogenität und Menge hat sich als große Herausforderung herausgestellt.
We report the results of a Versailles Project on Advanced Materials and Standards (VAMAS) interlaboratory study on the measurement of the shell thickness and chemistry of nanoparticle coatings. Peptide-coated gold particles were supplied to laboratories in two forms: a colloidal suspension in pure water and particles dried onto a silicon wafer. Participants prepared and analyzed these samples using either X-ray photoelectron spectroscopy (XPS) or low energy ion scattering (LEIS). Careful data analysis revealed some significant sources of discrepancy, particularly for XPS. Degradation during transportation, storage, or sample preparation resulted in a variability in thickness of 53%. The calculation method chosen by XPS participants contributed a variability of 67%. However, variability of 12% was achieved for the samples deposited using a single method and by choosing photoelectron peaks that were not adversely affected by instrumental transmission effects. The study identified a need for more consistency in instrumental transmission functions and relative sensitivity factors since this contributed a variability of 33%. The results from the LEIS participants were more consistent, with variability of less than 10% in thickness, and this is mostly due to a common method of data analysis. The calculation was performed using a model developed for uniform, flat films, and some participants employed a correction factor to account for the sample geometry, which appears warranted based upon a simulation of LEIS data from one of the participants and comparison to the XPS results.
In recent years, thermoextraction/desorption-gas chromatography/mass spectrometry (TED-GC/MS) has been developed as a rapid detection method for the determination of microplastics (MP) mass contents in numerous environmentally relevant matrices and, in particular, for the measurement of polymers in water samples without time-consuming sample preparation. The TED-GC/MS method was applied to investigate a typical European municipal wastewater system for possible MP masses. Such investigations are important in view of the recent revision of the Urban Wastewater Treatment Directive. Four different representative sampling sites were selected: greywater (domestic wastewater without toilet), combined sewer, and influent and effluent of a wastewater treatment plant (WWTP). All samples were collected by fractional filtration. Filtration was carried out over mesh sizes of 500, 100, 50, and in some cases, 5 µm. Polyethylene (PE), polypropylene (PP), and polystyrene (PS) were detected in all samples, with the PE fraction dominating in all cases. Styrene-butadiene rubber which serves as an indication of tire abrasion, was only found in the influent of the WWTP. The highest MP mass contents were found in the combined sewer, so MP can become a source of pollution during heavy rain events when the capacity limits of the effluent are reached, and the polluted effluent is released uncontrolled into the environment. Based on the studies, MP retention from the WWTP could be estimated to be approximately 96%. Few trends in polymer type or mass contents were detected within the different fractions of the samples or when comparing samples to each other.
Silicon photonic micro-ring resonators (MRR) developed on the silicon-on-insulator (SOI) platform, owing to their high sensitivity and small footprint, show great potential for many chemical and biological sensing applications such as label-free detection in environmental monitoring, biomedical engineering, and food analysis. In this tutorial,we provide the theoretical background and give design guidelines for SOI-based MRR as well as examples of surface functionalization procedures for label-free detection of molecules. After introducing the advantages and perspectives of MRR, fundamentals of MRR are described in detail, followed by an introduction to the fabrication methods, which are based on a complementary metal-oxide semiconductor (CMOS) technology. Optimization of MRR for chemical and biological sensing is provided, with special emphasis on the optimization of waveguide geometry. At this point, the difference between chemical bulk sensing and label-free surface sensing is explained, and definitions like waveguide sensitivity, ring sensitivity, overall sensitivity as well as the limit of detection (LoD) of MRR are introduced. Further, we show and explain chemical bulk sensing of sodium chloride (NaCl) in water and provide a recipe for label-free surface sensing.
Silicon photonic micro-ring resonators (MRR) developed on the silicon-on-insulator (SOI) platform, owing to their high sensitivity and small footprint, show great potential for many chemical and biological sensing applications such as label-free detection in environmental monitoring, biomedical engineering, and food analysis. In this tutorial, we provide the theoretical background and give design guidelines for SOI-based MRR as well as examples of surface functionalization procedures for label-free detection of molecules.
After introducing the advantages and perspectives of MRR, fundamentals of MRR are described in detail, followed by an introduction to the fabrication methods, which are based on a complementary metal-oxide semiconductor (CMOS) technology. Optimization of MRR for chemical and biological sensing is provided, with special emphasis on the optimization of waveguide geometry. At this point, the difference between chemical bulk sensing and label-free surface sensing is explained, and definitions like waveguide sensitivity, ring sensitivity, overall sensitivity as well as the limit of detection (LoD) of MRR are introduced. Further, we show and explain chemical bulk sensing of sodium chloride (NaCl) in water and provide a recipe for label-free surface sensing.
Cardiac troponin I (cTnI) is a crucial biomarker for diagnosing cardiac vascular diseases, including acute myocardial infarction (AMI). This study presents a proof-of-concept chemiluminescence-based immunosensor for rapid and accurate measurement of cTnI, with the potential for online monitoring. The immunosensor incorporates a flow cell design and a sensitive complementary metal-oxide-semiconductor (CMOS) camera for optical readout. A microfluidic setup was established to enable selective and quasi-online determination of cTnI within ten minutes. The sensor was tested with recombinant cTnI in phosphate buffer, demonstrating measurements in the concentration range of 2–25 µg/L, with a limit of detection (LoD) of 0.6 µg/L (23 pmol/L) achieved using the optimized system. The immunosensor exhibited high selectivity, as no cross-reactivity was observed with other recombinant proteins such as cTnT and cTnC at a concentration of 16 µg/L. Measurements with diluted blood plasma and serum yielded an LoD of 60 µg/L (2.4 nmol/L) and 70 µg/L (2.9 nmol/L), respectively. This biosensor offers a promising approach for the rapid and sensitive detection of cTnI, contributing to the diagnosis and management of acute myocardial infarction and other cardiac vascular diseases.
Using fluorescence-guided surgery (FGS) to cytoreductive surgery helps achieving complete resection of microscopic ovarian tumors. The use of visible and NIR-I fluorophores has led to beneficial results in clinical trials; however, involving NIR-II dyes seems to outperform those benefits due to the deeper tissue imaging and higher signal/noise ratio attained within the NIR-II optical window. In this context, we developed NIR-II emitting dyes targeting human epidermal growth factor receptor 2 (HER2)-positive ovarian tumors by coupling water-soluble NIR-II aza-BODIPY dyes to the FDA-approved anti-HER2 antibody, namely, trastuzumab. These bioconjugated NIR-II-emitting dyes displayed a prolonged stability in serum and a maintained affinity toward HER2 in vitro. We obtained selective targeting of HER2 positive tumors (SKOV-3) in vivo, with a favorable tumor accumulation. We demonstrated the fluorescence properties and the specific HER2 binding of the bioconjugated dyes in vivo and thus their potential for NIR-II FGS in the cancer setting.
An investigation of microplastic (MP) occurrence in a municipal wastewater treatment plant (WWTP) effluent with tertiary treatment was carried out. Representative sample volumes of 1 m3 were taken by applying a fractionated filtration method (500, 100, and 50 µm mesh sizes). The detection of MP mass fractions by thermal extraction desorption–gas chromatography/mass spectrometry (TED-GC/MS) was achieved without the previously required additional sample pretreatment for the first time. Different types of quantification methods for the evaluation of TED-GC/MS data were tested, and their accuracy and feasibility have been proven for real samples. Polyethylene, polystyrene, and polypropylene were identified in effluent samples. The polymer mass content varied significantly between 5 and 50 mg m−3. A correlation between the MP load and the quantity of suspended matter in the WWTP effluents, particle size distribution, particle type, and operation day (i.e., weekday, season, and capacity) was not found. It can be concluded that a meaningful assessment of WWTPs requires a comprehensive sampling campaign with varying operation conditions.