-
Journal of Structural Biology Sep 2023This paper introduces OpenFIBSEM, a universal API to control Focused Ion Beam Scanning Electron Microscopes (FIBSEM). OpenFIBSEM aims to improve the programmability and...
This paper introduces OpenFIBSEM, a universal API to control Focused Ion Beam Scanning Electron Microscopes (FIBSEM). OpenFIBSEM aims to improve the programmability and automation of electron microscopy workflows in structural biology research. The API is designed to be cross-platform, composable, and extendable: allowing users to use any portion of OpenFIBSEM to develop or integrate with other software tools. The package provides core functionality such as imaging, movement, milling, and manipulator control, as well as system calibration, alignment, and image analysis modules. Further, a library of reusable user interface components integrated with napari is provided, ensuring easy and efficient application development. OpenFIBSEM currently supports ThermoFisher and TESCAN hardware, with support for other manufacturers planned. To demonstrate the improved automation capabilities enabled by OpenFIBSEM, several example applications that are compatible with multiple hardware manufacturers are discussed. We argue that OpenFIBSEM provides the foundation for a cross-platform operating system and development ecosystem for FIBSEM systems. The API and applications are open-source and available on GitHub (https://github.com/DeMarcoLab/fibsem).
Topics: Ecosystem; Software; Microscopy; Automation; Image Processing, Computer-Assisted
PubMed: 37105276
DOI: 10.1016/j.jsb.2023.107967 -
International Journal of Molecular... Nov 2023Chromatin is now regarded as a heterogeneous and dynamic structure occupying a non-random position within the cell nucleus, where it plays a key role in regulating... (Review)
Review
Chromatin is now regarded as a heterogeneous and dynamic structure occupying a non-random position within the cell nucleus, where it plays a key role in regulating various functions of the genome. This current view of chromatin has emerged thanks to high spatiotemporal resolution imaging, among other new technologies developed in the last decade. In addition to challenging early assumptions of chromatin being regular and static, high spatiotemporal resolution imaging made it possible to visualize and characterize different chromatin structures such as clutches, domains and compartments. More specifically, super-resolution microscopy facilitates the study of different cellular processes at a nucleosome scale, providing a multi-scale view of chromatin behavior within the nucleus in different environments. In this review, we describe recent imaging techniques to study the dynamic organization of chromatin at high spatiotemporal resolution. We also discuss recent findings, elucidated by these techniques, on the chromatin landscape during different cellular processes, with an emphasis on the DNA damage response.
Topics: Chromatin; Nucleosomes; Microscopy; Genome; Cell Nucleus
PubMed: 37958958
DOI: 10.3390/ijms242115975 -
Histochemistry and Cell Biology Sep 2023Bioimaging has now entered the era of big data with faster-than-ever development of complex microscopy technologies leading to increasingly complex datasets. This... (Review)
Review
Bioimaging has now entered the era of big data with faster-than-ever development of complex microscopy technologies leading to increasingly complex datasets. This enormous increase in data size and informational complexity within those datasets has brought with it several difficulties in terms of common and harmonized data handling, analysis, and management practices, which are currently hampering the full potential of image data being realized. Here, we outline a wide range of efforts and solutions currently being developed by the microscopy community to address these challenges on the path towards FAIR bioimaging data. We also highlight how different actors in the microscopy ecosystem are working together, creating synergies that develop new approaches, and how research infrastructures, such as Euro-BioImaging, are fostering these interactions to shape the field.
Topics: Ecosystem; Microscopy
PubMed: 37341795
DOI: 10.1007/s00418-023-02203-7 -
Optics Express Sep 2023A technical challenge in neuroscience is to record and specifically manipulate the activity of neurons in living animals. This can be achieved in some preparations with...
A technical challenge in neuroscience is to record and specifically manipulate the activity of neurons in living animals. This can be achieved in some preparations with two-photon calcium imaging and photostimulation. These methods can be extended to three dimensions by holographic light sculpting with spatial light modulators (SLMs). At the same time, performing simultaneous holographic imaging and photostimulation is still cumbersome, requiring two light paths with separate SLMs. Here we present an integrated optical design using a single SLM for simultaneous imaging and photostimulation. Furthermore, we applied axially dependent adaptive optics to make the system aberration-free, and developed software for calibrations and closed-loop neuroscience experiments. Finally, we demonstrate the performance of the system with simultaneous calcium imaging and optogenetics in mouse primary auditory cortex in vivo. Our integrated holographic system could facilitate the systematic investigation of neural circuit function in awake behaving animals.
Topics: Animals; Mice; Calcium; Holography; Photons; Software; Neurons
PubMed: 37859128
DOI: 10.1364/OE.498051 -
Scientific Reports Nov 2023The purpose of this study was to investigate and compare the optical performance of five trifocal intraocular lenses (IOLs) following the ISO 11979-2 standards,...
The purpose of this study was to investigate and compare the optical performance of five trifocal intraocular lenses (IOLs) following the ISO 11979-2 standards, analysing the impact of tilt and decentration. Five different diffractive trifocal IOLs were evaluated in this experimental study: Acriva Trinova (VSY-Biotechnology) (AT), FineVision HP (PhysIOL) (FVHP), AT LISA tri 839 MP (Zeiss) (ATLT), PanOptix TFNT00 IOL (Alcon) (PO), and Tecnis Synergy (J&J Vision) (TS). In-vitro optical quality analysis of them was performed with the Lambda PMTF system that has an aberration neutral cornea model (Lambda-X Ophthalmics). Measurements were performed on-axis, with 5º of IOL tilt and with 0.5 mm of IOL decentration using 543-nm monochromatic light. Finally, IOL dimensions and diffractive disk profile inspection was performed using the VisIOLA system (Rotlex). On-axis measurements showed a far through-focus MTF > 0.3 at 3 mm aperture, except for TS. FVHP and PO showed better far MTFs for larger apertures (3.75 mm and 4.5 mm) while AT showed good intermediate and near vision for such apertures. With 5º of IOL tilt, the better optical performance at all distances was found with AT for medium-sized pupils (3 mm) and an important reduction of MTF was found for ATLT and PO, especially in the intermediate focus. The induction of 0.5 mm of IOL decentration especially affected the intermediate focus of ATLT and TS and the far focus of FVHP and PO. IOL dimensions and diffractive profile were consistent with those described by the manufacturer. In conclusion, there are differences in the optical performance according to the pupil aperture of the five trifocal IOLs evaluated and this should be considered in clinical practice when selecting the most appropriate implant in each specific case. IOL tilt and decentration can affect significantly in most of the designs evaluated the performance of the IOL at intermediate vision range. It should be noted that measurements were made with an aberration-free cornea, being necessary future studies analysing the impact of different levels of corneal aberrations.
Topics: Prosthesis Design; Optics and Photonics; Lenses, Intraocular; Multifocal Intraocular Lenses; Pupil
PubMed: 37950090
DOI: 10.1038/s41598-023-47102-y -
International Journal of Molecular... Dec 2023Optical nanoscopy, also known as super-resolution optical microscopy, has provided scientists with the means to surpass the diffraction limit of light microscopy and... (Review)
Review
Optical nanoscopy, also known as super-resolution optical microscopy, has provided scientists with the means to surpass the diffraction limit of light microscopy and attain new insights into nanoscopic structures and processes that were previously inaccessible. In recent decades, numerous studies have endeavored to enhance super-resolution microscopy in terms of its spatial (lateral) resolution, axial resolution, and temporal resolution. In this review, we discuss recent efforts to push the resolution limit of stimulated emission depletion (STED) optical nanoscopy across multiple dimensions, including lateral resolution, axial resolution, temporal resolution, and labeling precision. We introduce promising techniques and methodologies building on the STED concept that have emerged in the field, such as MINSTED, isotropic STED, and event-triggered STED, and evaluate their respective strengths and limitations. Moreover, we discuss trade-off relationships that exist in far-field optical microscopy and how they come about in STED optical nanoscopy. By examining the latest developments addressing these aspects, we aim to provide an updated overview of the current state of STED nanoscopy and its potential for future research.
Topics: Microscopy
PubMed: 38203197
DOI: 10.3390/ijms25010026 -
Nature Jul 2023Photosynthesis is generally assumed to be initiated by a single photon from the Sun, which, as a weak light source, delivers at most a few tens of photons per nanometre...
Photosynthesis is generally assumed to be initiated by a single photon from the Sun, which, as a weak light source, delivers at most a few tens of photons per nanometre squared per second within a chlorophyll absorption band. Yet much experimental and theoretical work over the past 40 years has explored the events during photosynthesis subsequent to absorption of light from intense, ultrashort laser pulses. Here, we use single photons to excite under ambient conditions the light-harvesting 2 (LH2) complex of the purple bacterium Rhodobacter sphaeroides, comprising B800 and B850 rings that contain 9 and 18 bacteriochlorophyll molecules, respectively. Excitation of the B800 ring leads to electronic energy transfer to the B850 ring in approximately 0.7 ps, followed by rapid B850-to-B850 energy transfer on an approximately 100-fs timescale and light emission at 850-875 nm (refs. ). Using a heralded single-photon source along with coincidence counting, we establish time correlation functions for B800 excitation and B850 fluorescence emission and demonstrate that both events involve single photons. We also find that the probability distribution of the number of heralds per detected fluorescence photon supports the view that a single photon can upon absorption drive the subsequent energy transfer and fluorescence emission and hence, by extension, the primary charge separation of photosynthesis. An analytical stochastic model and a Monte Carlo numerical model capture the data, further confirming that absorption of single photons is correlated with emission of single photons in a natural light-harvesting complex.
Topics: Bacterial Proteins; Bacteriochlorophylls; Energy Transfer; Light-Harvesting Protein Complexes; Photons; Rhodobacter sphaeroides; Photosynthesis; Fluorescence; Stochastic Processes; Monte Carlo Method
PubMed: 37316658
DOI: 10.1038/s41586-023-06121-5 -
Journal of Biomedical Optics Dec 2023Medical imaging is very commonly described as synonymous with radiological imaging, yet optical imaging devices are widely distributed throughout many medical...
SIGNIFICANCE
Medical imaging is very commonly described as synonymous with radiological imaging, yet optical imaging devices are widely distributed throughout many medical specialties. This delocalized nature of the technology reduces visibility and dominance as a cohesive medical technology sector.
AIM
Indicators of impact of medical optical systems were examined and compared to the radiology technology sector.
APPROACH
This study included a summary of (i) physician users, (ii) global technology valuations, and (iii) NIH funding levels. Analysis focused on comparing optical and radiological technology, comparing costs, funding, and finding differences, while tabulating strengths, weaknesses, opportunities, and threats to the field of optical imaging.
RESULTS
The 2023 global technology revenue valuation of biomedical optical tools is $128 billion USD/year while that of radiological tools is $48 billion USD/year. A direct comparison of US NIH funding in radiology shows $8.5 billion/year, whereas optical devices are nearer to $3.6 billion USD/year. R&D investment in applications, such as endoscopy, laparoscopy, and pulse oximetry, is far below those of radiological tools when normalized by valuation.
CONCLUSIONS
The medical optical device industry is highly fragmented but has become the largest single technology sector in medicine today. When contrasted to radiology, it appears underfunded for research, where point-of-care tools such as surgery, endoscopy, laparoscopy, ophthalmology, pulse oximetry, and monitoring have more potential for development through research investment.
Topics: Diagnostic Imaging; Radiography; Optics and Photonics
PubMed: 37780842
DOI: 10.1117/1.JBO.28.12.121208 -
Sensors (Basel, Switzerland) Jul 2023This paper presents reported machine learning approaches in the field of Brillouin distributed fiber optic sensors (DFOSs). The increasing popularity of Brillouin DFOSs... (Review)
Review
This paper presents reported machine learning approaches in the field of Brillouin distributed fiber optic sensors (DFOSs). The increasing popularity of Brillouin DFOSs stems from their capability to continuously monitor temperature and strain along kilometer-long optical fibers, rendering them attractive for industrial applications, such as the structural health monitoring of large civil infrastructures and pipelines. In recent years, machine learning has been integrated into the Brillouin DFOS signal processing, resulting in fast and enhanced temperature, strain, and humidity measurements without increasing the system's cost. Machine learning has also contributed to enhanced spatial resolution in Brillouin optical time domain analysis (BOTDA) systems and shorter measurement times in Brillouin optical frequency domain analysis (BOFDA) systems. This paper provides an overview of the applied machine learning methodologies in Brillouin DFOSs, as well as future perspectives in this area.
Topics: Fiber Optic Technology; Optical Devices; Optical Fibers; Humidity; Machine Learning
PubMed: 37448034
DOI: 10.3390/s23136187 -
Radiation Protection Dosimetry Sep 2023Biomarkers for ionising radiation exposure have great utility in scenarios where there has been a potential exposure and physical dosimetry is missing or in dispute,...
Biomarkers for ionising radiation exposure have great utility in scenarios where there has been a potential exposure and physical dosimetry is missing or in dispute, such as for occupational and accidental exposures. Biomarkers that respond as a function of dose are particularly useful as biodosemeters to determine the dose of radiation to which an individual has been exposed. These dose measurements can also be used in medical scenarios to track doses from medical exposures and even have the potential to identify an individual's response to radiation exposure that could help tailor treatments. The measurement of biomarkers of exposure in medicine and for accidents, where a larger number of samples would be required, is limited by the throughput of analysis (i.e. the number of samples that could be processed and analysed), particularly for microscope-based methods, which tend to be labour-intensive. Rapid analysis in an emergency scenario, such as a large-scale accident, would provide dose estimates to medical practitioners, allowing timely administration of the appropriate medical countermeasures to help mitigate the effects of radiation exposure. In order to improve sample throughput for biomarker analysis, much effort has been devoted to automating the process from sample preparation through automated image analysis. This paper will focus mainly on biological endpoints traditionally analysed by microscopy, specifically dicentric chromosomes, micronuclei and gamma-H2AX. These endpoints provide examples where sample throughput has been improved through automated image acquisition, analysis of images acquired by microscopy, as well as methods that have been developed for analysis using imaging flow cytometry.
Topics: Humans; Flow Cytometry; Health Personnel; Image Processing, Computer-Assisted; Medicine; Microscopy
PubMed: 37721060
DOI: 10.1093/rpd/ncad060