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High-throughput, high-content imaging technologies and multiplex slide scanning have become widely used. Advantages of these approaches include the ability to archive digital copies of slides, review slides as teams using virtual microscopy software, and standardize analytical approaches. The cost and hardware and software inflexibility of dedicated slide scanning devices can, however, complicate implementation. Here, we describe a simple method that allows any microscope to be used for slide scanning. The only requirements are that the microscope be equipped with a motorized filter turret or wheels (for multi-channel fluorescence) and a motorized xyz stage. This example uses MetaMorph software, but the same principles can be used with any microscope control software that includes a few standard functions and allows programming of simple command routines, or journals. The series of journals that implement the method perform key functions, including assistance in defining an unlimited number of regions of interest (ROI) and imaging parameters. Fully automated acquisition is rapid, taking less than 3 hr to image fifty 2.5-mm ROIs in four channels. Following acquisition, images can be easily stitched and displayed using open-source or commercial image-processing and virtual microscope applications. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Hardware and software configuration Basic Protocol 2: Create a preliminary scan Basic Protocol 3: Select, save, and position ROIs Basic Protocol 4: Determine and set autofocus parameters Basic Protocol 5: Acquire tiled images Basic Protocol 6: Review the scans Basic Protocol 7: Reimage ROIs as needed Basic Protocol 8: Stitch, stack, and assemble images Basic Protocol 9: Repeat scanning for multiplex immunostaining or background subtraction.

Funding: The experimental work has been supported by the European Research Council (ERC), the Scottish Funding Council, the UK EPSRC and the Swiss National Science Foundation (SNSF). Theoretical work was supported by the ERC grant ERC-319286-QMAC and by the SNSF (NCCR MARVEL).

We explore the interplay of electron-electron correlations and spin-orbit coupling in the model Fermi liquid Sr2RuO4 using laser-based angle-resolved photoemission spectroscopy. Our precise measurement of the Fermi surface confirms the importance of spin-orbit coupling in this material and reveals that its effective value is enhanced by a factor of about two, due to electronic correlations. The self-energies for the $\beta$ and $\gamma$ sheets are found to display significant angular dependence. By taking into account the multi-orbital composition of quasiparticle states, we determine self-energies associated with each orbital component directly from the experimental data. This analysis demonstrates that the perceived angular dependence does not imply momentum-dependent many-body effects, but arises from a substantial orbital mixing induced by spin-orbit coupling. A comparison to single-site dynamical mean-field theory further supports the notion of dominantly local orbital self-energies, and provides strong evidence for an electronic origin of the observed non-linear frequency dependence of the self-energies, leading to `kinks' in the quasiparticle dispersion of Sr2RuO4., Comment: PRX accepted

Primitive streak formation in the chick embryo involves large-scale highly coordinated flows of more than 100,000 cells in the epiblast. These large-scale tissue flows and deformations can be correlated with specific anisotropic cell behaviours in the forming mesendoderm through a combination of light-sheet microscopy and computational analysis. Relevant behaviours include apical contraction, elongation along the apical-basal axis followed by ingression, and asynchronous directional cell intercalation of small groups of mesendoderm cells. Cell intercalation is associated with sequential, directional contraction of apical junctions, the onset, localization and direction of which correlate strongly with the appearance of active myosin II cables in aligned apical junctions in neighbouring cells. Use of class specific myosin inhibitors and gene-specific knockdown shows that apical contraction and intercalation are myosin II dependent and also reveal critical roles for myosin I and myosin V family members in the assembly of junctional myosin II cables.

Despite significant advances in biological imaging and analysis, major informatics challenges remain unsolved: file formats are proprietary, storage and analysis facilities are lacking, as are standards for sharing image data and results. While the open FITS file format is ubiquitous in astronomy, astronomical imaging shares many challenges with biological imaging, including the need to share large image sets using secure, cross-platform APIs, and the need for scalable applications for processing and visualization. The Open Microscopy Environment (OME) is an open-source software framework developed to address these challenges. OME tools include: an open data model for multidimensional imaging (OME Data Model); an open file format (OME-TIFF) and library (Bio-Formats) enabling free access to images (5D+) written in more than 145 formats from many imaging domains, including FITS; and a data management server (OMERO). The Java-based OMERO client-server platform comprises an image metadata store, an image repository, visualization and analysis by remote access, allowing sharing and publishing of image data. OMERO provides a means to manage the data through a multi-platform API. OMERO’s model-based architecture has enabled its extension into a range of imaging domains, including light and electron microscopy, high content screening, digital pathology and recently into applications using non-image data from clinical and genomic studies. This is made possible using the Bio-Formats library. The current release includes a single mechanism for accessing image data of all types, regardless of original file format, via Java, C/C++ and Python and a variety of applications and environments (e.g. ImageJ, Matlab and R).

We study the process of excitation transfer between vertically stacked dots due to the combined effect of the Forster coupling and carrier–phonon interaction. A consistent Markovian approximation is derived which reasonably reproduces the quantum-kinetic results. The impact of the exciton transfer process on the temperature-dependent intensity of spectral lines is discussed in terms of rate equations. (© 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

The Open Microscopy Environment (OME) has built and released Bio-Formats, a Java-based proprietary file format conversion tool and OMERO, an enterprise data management platform under open source licenses. In this report, we describe new versions of Bio-Formats and OMERO that are specifically designed to support large, multi-gigabyte or terabyte scale datasets that are routinely collected across most domains of biological and biomedical research. Bio- Formats reads image data directly from native proprietary formats, bypassing the need for conversion into a standard format. It implements the concept of a file set, a container that defines the contents of multi-dimensional data comprised of many files. OMERO uses Bio-Formats to read files natively, and provides a flexible access mechanism that supports several different storage and access strategies. These new capabilities of OMERO and Bio-Formats make them especially useful for use in imaging applications like digital pathology, high content screening and light sheet microscopy that create routinely large datasets that must be managed and analyzed.

We investigate the bilayer Ruddlesden-Popper iridate Sr${}_{3}$Ir${}_{2}$O${}_{7}$ by temperature-dependent angle-resolved photoemission. At low temperatures, we find a fully gapped correlated insulator, characterized by a small charge gap and narrow bandwidths. The low-energy spectral features show a pronounced temperature-dependent broadening and non-quasiparticle-like Gaussian line shapes. Together, these spectral features provide experimental evidence for a polaronic ground state. We observe similar behavior for the single-layer cousin Sr${}_{2}$IrO${}_{4}$, indicating that strong electron-boson coupling dominates the low-energy excitations of this exotic family of $5d$ compounds.

We present angle-resolved photoemission data from Cu(111). Using a focused 6 eV continuous wave laser for photo-excitation, we achieve a high effective momentum resolution enabling the first detection of the Rashba spin splitting in the Shockley surface state on Cu(111). The magnitude of the spin-splitting of Delta k ~ 0.006 A^-1 is surprisingly large and exceeds values predicted for the analogous surface state on Ag(111) but is reproduced by first principles calculations. We further resolve a kink in the dispersion which we attribute to electron-phonon coupling., Comment: 5 pages, 3 figures, to appear in Phys. Rev. B

We observe apparent hole pockets in the Fermi surfaces of single-layer Bi-based cuprate superconductors from angle-resolved photoemission. From detailed low-energy electron diffraction measurements and an analysis of the angle-resolved photoemission polarization dependence, we show that these pockets are not intrinsic but arise from multiple overlapping superstructure replicas of the main and shadow bands. We further demonstrate that the hole pockets reported recently from angle-resolved photoemission [Meng et al., Nature (London) 462, 335 (2009)] have a similar structural origin and are inconsistent with an intrinsic hole pocket associated with the electronic structure of a doped ${\mathrm{CuO}}_{2}$ plane.

We observe apparent hole pockets in the Fermi surfaces of single-layer Bi-based cuprate superconductors from angle-resolved photoemission. From detailed low-energy electron diffraction measurements and an analysis of the angle-resolved photoemission polarization dependence, we show that these pockets are not intrinsic but arise from multiple overlapping superstructure replicas of the main and shadow bands. We further demonstrate that the hole pockets reported recently from angle-resolved photoemission [Meng et al., Nature (London) 462, 335 (2009)] have a similar structural origin and are inconsistent with an intrinsic hole pocket associated with the electronic structure of a doped CuO₂ plane.

We investigate the normal state of the ``11'' iron-based superconductor ${\mathrm{FeSe}}_{0.42}{\mathrm{Te}}_{0.58}$ by angle-resolved photoemission. Our data reveal a highly renormalized quasiparticle dispersion characteristic of a strongly correlated metal. We find sheet dependent effective carrier masses between $\ensuremath{\approx}3\text{ }\mathrm{\text{and}}\text{ }16{m}_{e}$ corresponding to a mass enhancement over band structure values of ${m}^{*}/{m}_{\mathrm{band}}\ensuremath{\approx}6--20$. This is nearly an order of magnitude higher than the renormalization reported previously for iron-arsenide superconductors of the ``1111'' and ``122'' families but fully consistent with the bulk specific heat.

We investigate the normal state of the "11" iron-based superconductor FeSe0.42Te0.58 by angle-resolved photoemission. Our data reveal a highly renormalized quasiparticle dispersion characteristic of a strongly correlated metal. We find sheet dependent effective carrier masses between approximately 3 and 16m{e} corresponding to a mass enhancement over band structure values of m{*}/m{band} approximately 6-20. This is nearly an order of magnitude higher than the renormalization reported previously for iron-arsenide superconductors of the "1111" and "122" families but fully consistent with the bulk specific heat.

We present a quantum-kinetic theory of the excitation transfer in a quantum dot molecule. We derive the consistent Markovian limit for the system kinetics, which leads to a description in terms of a single transfer rate for weak coupling. We show that the transfer rate is a strongly varying, nonmonotonic function of the spatial separation and energy mismatch between the dots.

We derive a quantum-kinetic description of phonon-assisted F{\"o}rster transfer between two coupled quantum dots (a quantum dot molecule). We show that the exciton state decays to the ground state of the QDM via a combination of the Rabi rotation and exponential decay. For moderately spaced dots this process takes place on a picosecond time scale., Comment: To be presented at the school Jaszowiec 2007

The production of crops capable of efficient nutrient use is essential for addressing the problem of global food security. The ability of a plant's root system to interact with the soil micro-environment determines how effectively it can extract water and nutrients. In order to assess this ability and develop the fast and cost effective phenotyping techniques which are needed to establish efficient root systems, in situ imaging in soil is required. To date this has not been possible due to the high density of scatterers and absorbers in soil or because other growth substrates do not sufficiently model the heterogeneity of a soil's microenvironment. We present here a new form of light sheet imaging with novel transparent soil containing refractive index matched particles. This imaging method does not rely on fluorescence, but relies solely on scattering from root material. We term this form of imaging Light Sheet Tomography (LST). We have tested LST on a range of materials and plant roots in transparent soil and gel. Due to the low density of root structures, i.e. relatively large spaces between adjacent roots, long-term monitoring of lettuce root development in situ with subsequent quantitative analysis was achieved.

We compare the relativistic LDA Fermi surface of Sr2RuO4 to direct experimental evidence of spin-orbit coupling from de Haas-van Alphen experiments. The k-dependence of the Zeeman splitting at the Fermi surface is modelled with a range of tight binding models of the quasi-particle bands. Only a very restricted class of parameters are consistent with evidence from the de Haas-van Alphen experiments for a strong k-dependent Zeeman splitting on the alpha Fermi surface sheet. The bare LDA bands do not lead to such a strong k-dependent Zeeman splitting on this sheet, and this suggests that additional charge transfer takes place as suggested by DMFT calculations. We conclude that the overall scale of the spin-orbit coupling must be at least as large as the several hundred kelvin deduced in previous work, and that this must call into question any theory postulating rotation of the triplet d-vector at small magnetic fields.