Journal of microscopy最新文献

Modern bioimaging core facilities at research institutions are essential for managing and maintaining high-end instruments, providing training and support for researchers in experimental design, image acquisition and data analysis. An important task for these facilities is the professional management of complex multidimensional bioimaging data, which are often produced in large quantity and very different file formats. This article details the process that led to successfully implementing the OME Remote Objects system (OMERO) for bioimage-specific research data management (RDM) at the Core Facility Cellular Imaging (CFCI) at the Technische Universität Dresden (TU Dresden). Ensuring compliance with the FAIR (findable, accessible, interoperable, reusable) principles, we outline here the challenges that we faced in adapting data handling and storage to a new RDM system. These challenges included the introduction of a standardised group-specific naming convention, metadata curation with tagging and Key–Value pairs, and integration of existing image processing workflows. By sharing our experiences, this article aims to provide insights and recommendations for both individual researchers and educational institutions intending to implement OMERO as a management system for bioimaging data. We showcase how tailored decisions and structured approaches lead to successful outcomes in RDM practices.

Lay description: Modern bioimaging facilities at research institutions are crucial for managing advanced equipment and supporting scientists in their research. These facilities help with designing experiments, capturing images, and analyzing data. One of their key tasks is organizing and managing large amounts of complex image data, which often comes in various file formats and are difficult to handle.

This article explains how the Core Facility Cellular Imaging (CFCI) at Technische Universität Dresden successfully implemented a specialized system called OMERO. With this system it is possible to manage and organize bioimaging data sustainably in a way that they are findable, accessible, interoperable and reusable according the FAIR principles. We describe the practical implementation process on exemplary projects within scientific research and medical education. We discuss the challenges we faced, such as creating a standard way to name files, organizing important information about the images (known as metadata), and ensuring that existing image processing methods could work with the new system.

By sharing our experience, we aim to offer practical advice and recommendations for other researchers and institutions interested in using OMERO for managing their bioimaging data. We highlight how careful planning and structured approaches can lead to successful data management practices, making it easier for researchers to store, access, and reuse their valuable data.

The endoplasmic reticulum (ER) is the largest organelle in terms of membrane content, occupying the entire cytoplasmic volume. It is tethered to the cell cortex through ER-plasma membrane contact sites (EPCS). Previous studies have shown that EPCSs labelled by VAP27 align with cortical microtubules, and that ER tubules elongate along microtubules. Here, we addressed the question whether this relationship is bidirectional, with EPCSs influencing microtubule organisation. Using TIRF microscopy to track EPCSs and microtubule dynamics simultaneously, we demonstrate that while EPCSs remain stable, microtubules are highly dynamic and can adjust their positioning based on nearby EPCS in Arabidopsis cotyledon epidermis. In lobes of epidermal cells enclosed by two indentations, where microtubules bundle together, EPCSs flank the bundles and exhibit a distinctive arrangement, forming symmetric arcs in relation to the lobe axis. In guard cells, transversely oriented ER tubules co-align with microtubules. Disrupting microtubules with the drug oryzalin leads to transient guard cells-ER remodelling, followed by its reorganisation into transverse tubules before microtubule recovery. Taken together our observations suggest, that the positioning of EPCSs and cortical microtubules, can affect each other and the organisation of cortical ER.

Roldan, D., Redenbach, C., Schladitz, K., Kübel, C., & Schlabach, S. (2024). Image quality evaluation for FIB-SEM images. Journal of Microscopy, 293(2), 98-117. https://onlinelibrary.wiley.com/doi/10.1111/jmi.13254

Diego Roldan's affiliation appears as “National University, Bogotá, Colombia”

The correct affiliation is “Departamento de Matemáticas, Universidad Nacional de Colombia, Bogotá, Colombia”

We apologise for this error.

Interferometric scattering (iSCAT) microscopy enables high-speed and label-free detection of individual molecules and small nanoparticles. Here we apply point spread function engineering to provide adaptive control of iSCAT images using spatial light modulation. With this approach, we demonstrate improved dynamic spatial filtering, real-time background subtraction, focus control, and signal modulation based on sample orientation.

Despite the widespread use of Scanning Transmission Electron Microscopy (STEM) for observing the structure of materials at the atomic scale, a detailed understanding of some relevant electron beam damage mechanisms is limited. Recent reports suggest that certain types of damage can be modelled as a diffusion process and that the accumulation effects of this process must be kept low in order to reduce damage. We therefore develop an explicit mathematical formulation of spatiotemporal diffusion processes in STEM that take into account both instrument and sample parameters. Furthermore, our framework can aid the design of Diffusion Controlled Sampling (DCS) strategies using optimally selected probe positions in STEM, that constrain the cumulative diffusion distribution. Numerical simulations highlight the variability of the cumulative diffusion distribution for different experimental STEM configurations. These analytical and numerical frameworks can subsequently be used for careful design of 2- and 4-dimensional STEM experiments where beam damage is minimised.

Chvalova, V., Vomastek, T., & Grousl, T. (2024). Comparison of holotomographic microscopy and coherence-controlled holographic microscopy. Journal of Microscopy, 294(1), 5–13. https://onlinelibrary.wiley.com/doi/10.1111/jmi.13260

In the Acknowledgements, the grant number “Ministry of Health project NU22-03-00197 (to TV)” was incorrect. This should have read: “Ministry of Health project NU23-03-00557 (to TV)”.

We apologise for this error.

A three-dimensional (3D) microstructural volume is reconstructed from a stack of two-dimensional sections which was obtained by serial sectioning coupled with electron back scattering diffraction (EBSD) mapping of a 316L austenitic stainless steel. A new alignment algorithm named linear translation by minimising the indicator (LTMI) is proposed to reduce the translational misalignments between adjacent sections by referencing to coherent twin boundaries which are flat and lying on {111} planes. The angular difference between the measured orientation of a flat twin boundary and that of the {111} plane is used as an indicator of the accuracy of the alignment operations. This indicator is minimised through linear translations of the centroids of triangular facets, which constitute grain boundaries at a distance not restricted by the in-plane step size of the EBSD maps. And hence the systematic trend in the translational misalignments can be effectively reduced. The LTMI alignment procedure proposed herein effectively corrects the misalignments remained by other methods on a 3D-EBSD data prepared using serial sectioning methods. The accuracy in distinguishing between coherent and incoherent twin boundaries is significantly improved.

Electron energy loss spectra collected from fresh and corroded silver nanoparticles are compared with those from a number of reference materials, focusing on the M_4,5 edge. Chemical shifts and changes in the energy loss near edge structure (ELNES) are described and found to be sufficient to distinguish metallic silver from chemically oxidised silver. The measurements, in conjunction with electron energy loss spectrum imaging, are used to assess the mechanisms for atmospheric corrosion of silver nanoparticles. We unambiguously assign the corrosion product under atmospheric conditions to be silver sulphide, but show the reaction process to be distinctly inhomogeneous, producing a variety of types of corroded particles.

LAY DESCRIPTION: >Here, we use analytical electron microscopy to track the corrosion of silver nanoparticles and present chemical maps of the corrosion products. We show clear spectroscopic differences between metallic and corroded silver using the M_4,5 electron energy loss spectral feature, which is not commonly studied. Our study shows that corrosion is due to interactions with sulphur in the atmosphere; and the corrosion is not uniform, but appears to develop from specific points on the surface of the nanoparticles.