Light Sheet Tomography (LST) for <i>in situ</i> imaging of plant roots

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

Publishing and sharing multi-dimensional image data with OMERO

Imaging data are used in the life and biomedical sciences to measure the molecular and structural composition and dynamics of cells, tissues, and organisms. Datasets range in size from megabytes to terabytes and usually contain a combination of binary pixel data and metadata that describe the acquisition process and any derived results. The OMERO image data management platform allows users to securely share image datasets according to specific permissions levels: data can be held privately, shared with a set of colleagues, or made available via a public URL. Users control access by assigning data to specific Groups with defined membership and access rights. OMERO’s Permission system supports simple data sharing in a lab, collaborative data analysis, and even teaching environments. OMERO software is open source and released by the OME Consortium at www.openmicroscopy.org

Metadata management for high content screening in OMERO

High content screening (HCS) experiments create a classic data management challenge—multiple, large sets of heterogeneous structured and unstructured data, that must be integrated and linked to produce a set of “final” results. These different data include images, reagents, protocols, analytic output, and phenotypes, all of which must be stored, linked and made accessible for users, scientists, collaborators and where appropriate the wider community. The OME Consortium has built several open source tools for managing, linking and sharing these different types of data. The OME Data Model is a metadata specification that supports the image data and metadata recorded in HCS experiments. Bio-Formats is a Java library that reads recorded image data and metadata and includes support for several HCS screening systems. OMERO is an enterprise data management application that integrates image data, experimental and analytic metadata and makes them accessible for visualization, mining, sharing and downstream analysis. We discuss how Bio-Formats and OMERO handle these different data types, and how they can be used to integrate, link and share HCS experiments in facilities and public data repositories. OME specifications and software are open source and are available at https://www.openmicroscopy.org

Effects of spin-orbit coupling and many-body interactions on the electronic structure of Sr₂RuO₄

The aim of the project is to investigate the effects of spin-orbit coupling and many-body interactions on the band structure of the single-layered strontium ruthenate Sr₂RuO₄. This material belongs to the large family of strongly correlated electron systems in which electron-electron interaction plays a crucial role in determining the macroscopic properties. The experimental method used for this purpose is Angular Resolved Photoemission Spectroscopy (ARPES), which probes the single-particle spectral function and allows direct measurements of the quasi-particle band structure. The analysis is based on comparison of experimental data with electronic structure calculations. Typical methods for the band structure calculations including density functional theory (DFT) in the local density approximation (LDA) and tight-binding calculations (TB) are one-electron approximations and do not give insight into many-body interactions. However, comparing the measured band structures with calculated ones allows estimating the strength of the interactions in the considered system. In Chapter 1 the earlier work on Sr₂RuO₄, which is relevant to this project is presented. This chapter is an introduction to the data analysis and discussion of the results. In Chapter 2 we describe the experimental setup, theoretical principles of the measurement and summarize important improvements made during this project. In Chapter 3 we give a brief introduction into density functional theory and describe methods used within DFT to calculate the band structure. We further give a brief description of a tight binding model for Sr₂RuO₄. The bulk of this chapter is devoted to present the effects of spin-orbit coupling on the band structure of Sr₂RuO₄. In particular, we use a tight binding model to simulate the anisotropy of the Zeeman splitting found experimentally. In Chapter 4 we present the ARPES results, their analysis and discussion. A particular focus is placed on the discussion of the surface layer Fermi surface topology and on the discovery of strong momentum dependence of the mass renormalization factors of the bulk β and γ bands

Spin-orbit coupling and k-dependent Zeeman splitting in strontium ruthenate

We compare the relativistic LDA Fermi surface of Sr(2)RuO(4) 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

Media 1: Light Sheet Tomography (LST) for in situ imaging of plant roots

Originally published in Optics Express on 15 July 2013 (oe-21-14-16239

Media 3: Light Sheet Tomography (LST) for in situ imaging of plant roots

Originally published in Optics Express on 15 July 2013 (oe-21-14-16239