TY - JOUR A1 - Griebel, Matthias A1 - Segebarth, Dennis A1 - Stein, Nikolai A1 - Schukraft, Nina A1 - Tovote, Philip A1 - Blum, Robert A1 - Flath, Christoph M. T1 - Deep learning-enabled segmentation of ambiguous bioimages with deepflash2 JF - Nature Communications N2 - Bioimages frequently exhibit low signal-to-noise ratios due to experimental conditions, specimen characteristics, and imaging trade-offs. Reliable segmentation of such ambiguous images is difficult and laborious. Here we introduce deepflash2, a deep learning-enabled segmentation tool for bioimage analysis. The tool addresses typical challenges that may arise during the training, evaluation, and application of deep learning models on ambiguous data. The tool’s training and evaluation pipeline uses multiple expert annotations and deep model ensembles to achieve accurate results. The application pipeline supports various use-cases for expert annotations and includes a quality assurance mechanism in the form of uncertainty measures. Benchmarked against other tools, deepflash2 offers both high predictive accuracy and efficient computational resource usage. The tool is built upon established deep learning libraries and enables sharing of trained model ensembles with the research community. deepflash2 aims to simplify the integration of deep learning into bioimage analysis projects while improving accuracy and reliability. KW - machine learning KW - microscopy KW - quality control KW - software Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-357286 VL - 14 ER - TY - JOUR A1 - Winter, Patrick M. A1 - Andelovic, Kristina A1 - Kampf, Thomas A1 - Hansmann, Jan A1 - Jakob, Peter Michael A1 - Bauer, Wolfgang Rudolf A1 - Zernecke, Alma A1 - Herold, Volker T1 - Simultaneous measurements of 3D wall shear stress and pulse wave velocity in the murine aortic arch JF - Journal of Cardiovascular Magnetic Resonance N2 - Purpose Wall shear stress (WSS) and pulse wave velocity (PWV) are important parameters to characterize blood flow in the vessel wall. Their quantification with flow-sensitive phase-contrast (PC) cardiovascular magnetic resonance (CMR), however, is time-consuming. Furthermore, the measurement of WSS requires high spatial resolution, whereas high temporal resolution is necessary for PWV measurements. For these reasons, PWV and WSS are challenging to measure in one CMR session, making it difficult to directly compare these parameters. By using a retrospective approach with a flexible reconstruction framework, we here aimed to simultaneously assess both PWV and WSS in the murine aortic arch from the same 4D flow measurement. Methods Flow was measured in the aortic arch of 18-week-old wildtype (n = 5) and ApoE\(^{−/−}\) mice (n = 5) with a self-navigated radial 4D-PC-CMR sequence. Retrospective data analysis was used to reconstruct the same dataset either at low spatial and high temporal resolution (PWV analysis) or high spatial and low temporal resolution (WSS analysis). To assess WSS, the aortic lumen was labeled by semi-automatically segmenting the reconstruction with high spatial resolution. WSS was determined from the spatial velocity gradients at the lumen surface. For calculation of the PWV, segmentation data was interpolated along the temporal dimension. Subsequently, PWV was quantified from the through-plane flow data using the multiple-points transit-time method. Reconstructions with varying frame rates and spatial resolutions were performed to investigate the influence of spatiotemporal resolution on the PWV and WSS quantification. Results 4D flow measurements were conducted in an acquisition time of only 35 min. Increased peak flow and peak WSS values and lower errors in PWV estimation were observed in the reconstructions with high temporal resolution. Aortic PWV was significantly increased in ApoE\(^{−/−}\) mice compared to the control group (1.7 ± 0.2 versus 2.6 ± 0.2 m/s, p < 0.001). Mean WSS magnitude values averaged over the aortic arch were (1.17 ± 0.07) N/m\(^2\) in wildtype mice and (1.27 ± 0.10) N/m\(^2\) in ApoE\(^{−/−}\) mice. Conclusion The post processing algorithm using the flexible reconstruction framework developed in this study permitted quantification of global PWV and 3D-WSS in a single acquisition. The possibility to assess both parameters in only 35 min will markedly improve the analyses and information content of in vivo measurements. KW - 4D flow KW - pulse wave velocity KW - wall shear stress KW - radial KW - self-navigation KW - mouse KW - aortic arch KW - atherosclerosis KW - mice KW - flow KW - plaque KW - CMR KW - quantification KW - microscopy Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-259152 VL - 23 IS - 1 ER - TY - JOUR A1 - Peters, Simon A1 - Kaiser, Lena A1 - Fink, Julian A1 - Schumacher, Fabian A1 - Perschin, Veronika A1 - Schlegel, Jan A1 - Sauer, Markus A1 - Stigloher, Christian A1 - Kleuser, Burkhard A1 - Seibel, Juergen A1 - Schubert-Unkmeir, Alexandra T1 - Click-correlative light and electron microscopy (click-AT-CLEM) for imaging and tracking azido-functionalized sphingolipids in bacteria JF - Scientific Reports N2 - Sphingolipids, including ceramides, are a diverse group of structurally related lipids composed of a sphingoid base backbone coupled to a fatty acid side chain and modified terminal hydroxyl group. Recently, it has been shown that sphingolipids show antimicrobial activity against a broad range of pathogenic microorganisms. The antimicrobial mechanism, however, remains so far elusive. Here, we introduce 'click-AT-CLEM', a labeling technique for correlated light and electron microscopy (CLEM) based on the super-resolution array tomography (srAT) approach and bio-orthogonal click chemistry for imaging of azido-tagged sphingolipids to directly visualize their interaction with the model Gram-negative bacterium Neisseria meningitidis at subcellular level. We observed ultrastructural damage of bacteria and disruption of the bacterial outer membrane induced by two azido-modified sphingolipids by scanning electron microscopy and transmission electron microscopy. Click-AT-CLEM imaging and mass spectrometry clearly revealed efficient incorporation of azido-tagged sphingolipids into the outer membrane of Gram-negative bacteria as underlying cause of their antimicrobial activity. KW - antimicrobials KW - biological techniques KW - imaging KW - microbiology KW - microbiology techniques KW - microscopy Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-259147 VL - 11 IS - 1 ER - TY - JOUR A1 - Drakopoulos, Antonios A1 - Decker, Michael T1 - Development and Biological Applications of Fluorescent Opioid Ligands JF - ChemPlusChem N2 - Opioid receptors (ORs) are classified among the oldest and best investigated drug targets due to their fundamental role in the treatment of pain and related disorders. ORs are divided in three conventional subtypes (μ, κ, δ) and the non‐classical nocicepetin receptor. All ORs are family A G protein‐coupled receptors (GPCRs), and are located on the cell surface. Modern biophysical methods use light to investigate physiological processes at organismal, cellular and subcellular level. Many of these methods rely on fluorescent ligands, thus highlighting their importance. This review addresses the advancements in the development of opioid fluorescent ligands and their use in biological, pharmacological and imaging applications. KW - biophysics KW - fluorescent ligands KW - imaging KW - microscopy KW - opioid receptors Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-216068 VL - 85 IS - 6 SP - 1354 EP - 1364 ER - TY - JOUR A1 - Brunk, Michael A1 - Sputh, Sebastian A1 - Doose, Sören A1 - van de Linde, Sebastian A1 - Terpitz, Ulrich T1 - HyphaTracker: An ImageJ toolbox for time-resolved analysis of spore germination in filamentous fungi JF - Scientific Reports N2 - The dynamics of early fungal development and its interference with physiological signals and environmental factors is yet poorly understood. Especially computational analysis tools for the evaluation of the process of early spore germination and germ tube formation are still lacking. For the time-resolved analysis of conidia germination of the filamentous ascomycete Fusarium fujikuroi we developed a straightforward toolbox implemented in ImageJ. It allows for processing of microscopic acquisitions (movies) of conidial germination starting with drift correction and data reduction prior to germling analysis. From the image time series germling related region of interests (ROIs) are extracted, which are analysed for their area, circularity, and timing. ROIs originating from germlings crossing other hyphae or the image boundaries are omitted during analysis. Each conidium/hypha is identified and related to its origin, thus allowing subsequent categorization. The efficiency of HyphaTracker was proofed and the accuracy was tested on simulated germlings at different signal-to-noise ratios. Bright-field microscopic images of conidial germination of rhodopsin-deficient F. fujikuroi mutants and their respective control strains were analysed with HyphaTracker. Consistent with our observation in earlier studies the CarO deficient mutant germinated earlier and grew faster than other, CarO expressing strains. KW - bioinformatics KW - cell growth KW - fungal biology KW - microscopy Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-221691 VL - 8 ER - TY - JOUR A1 - Grimm, Jonathan B. A1 - Klein, Teresa A1 - Kopek, Benjamin G. A1 - Shtengel, Gleb A1 - Hess, Harald F. A1 - Sauer, Markus A1 - Lavis, Luke D. T1 - Synthesis of a far-red photoactivatable silicon-containing rhodamine for super-resolution microscopy JF - Angewandte Chemie International Edition N2 - The rhodamine system is a flexible framework for building small‐molecule fluorescent probes. Changing N‐substitution patterns and replacing the xanthene oxygen with a dimethylsilicon moiety can shift the absorption and fluorescence emission maxima of rhodamine dyes to longer wavelengths. Acylation of the rhodamine nitrogen atoms forces the molecule to adopt a nonfluorescent lactone form, providing a convenient method to make fluorogenic compounds. Herein, we take advantage of all of these structural manipulations and describe a novel photoactivatable fluorophore based on a Si‐containing analogue of Q‐rhodamine. This probe is the first example of a “caged” Si‐rhodamine, exhibits higher photon counts compared to established localization microscopy dyes, and is sufficiently red‐shifted to allow multicolor imaging. The dye is a useful label for super‐resolution imaging and constitutes a new scaffold for far‐red fluorogenic molecules. KW - fluorophore KW - microscopy KW - photoactivation KW - Si-rhodamine KW - super-resolution imaging Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-191069 VL - 55 IS - 5 ER - TY - JOUR A1 - Sessi, Paolo A1 - Silkin, Vyacheslav M. A1 - Nechaev, Ilya A. A1 - Bathon, Thomas A1 - El-Kareh, Lydia A1 - Chulkov, Evgueni V. A1 - Echenique, Pedro M. A1 - Bode, Matthias T1 - Direct observation of many-body charge density oscillations in a two-dimensional electron gas JF - Nature Communications N2 - Quantum interference is a striking manifestation of one of the basic concepts of quantum mechanics: the particle-wave duality. A spectacular visualization of this effect is the standing wave pattern produced by elastic scattering of surface electrons around defects, which corresponds to a modulation of the electronic local density of states and can be imaged using a scanning tunnelling microscope. To date, quantum-interference measurements were mainly interpreted in terms of interfering electrons or holes of the underlying band-structure description. Here, by imaging energy-dependent standing-wave patterns at noble metal surfaces, we reveal, in addition to the conventional surface-state band, the existence of an 'anomalous' energy band with a well-defined dispersion. Its origin is explained by the presence of a satellite in the structure of the many-body spectral function, which is related to the acoustic surface plasmon. Visualizing the corresponding charge oscillations provides thus direct access to many-body interactions at the atomic scale. KW - scanning tunneling spectroscopy KW - acoustic surface plasmon KW - metal surfaces KW - Cu(111) KW - excitations KW - microscopy KW - local density KW - standing wave formation KW - states KW - steps Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-145246 VL - 6 IS - 8691 ER - TY - JOUR A1 - Nanguneri, Siddharth A1 - Flottmann, Benjamin A1 - Horstmann, Heinz A1 - Heilemann, Mike A1 - Kuner, Thomas T1 - Three-Dimensional, Tomographic Super-Resolution Fluorescence Imaging of Serially Sectioned Thick Samples JF - PLoS One N2 - Three-dimensional fluorescence imaging of thick tissue samples with near-molecular resolution remains a fundamental challenge in the life sciences. To tackle this, we developed tomoSTORM, an approach combining single-molecule localization-based super-resolution microscopy with array tomography of structurally intact brain tissue. Consecutive sections organized in a ribbon were serially imaged with a lateral resolution of 28 nm and an axial resolution of 40 nm in tissue volumes of up to 50 \(\mu\)mx50\(\mu\)mx2.5\(\mu\)m. Using targeted expression of membrane bound (m)GFP and immunohistochemistry at the calyx of Held, a model synapse for central glutamatergic neurotransmission, we delineated the course of the membrane and fine-structure of mitochondria. This method allows multiplexed super-resolution imaging in large tissue volumes with a resolution three orders of magnitude better than confocal microscopy. KW - architecture KW - rat calyx KW - in-vivo KW - microscopy KW - resolution KW - proteins KW - transmission KW - ultrastructure KW - reconstruction KW - localization Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-134434 VL - 7 IS - 5 ER -