A compact system for intraoperative specimen imaging based on edge illumination x-ray phase contrast

“This is an author-created, un-copyedited version of an article accepted for publication/published in Physics in Medicine & Biology. IOP Publishing Ltd is not responsible for any errors or omissions in this version of the manuscript or any version derived from it. The Version of Record is available online at https://doi.org/10.1088/1361-6560/ab4912

Development of Electron Bunch Compression Monitors for SwissFEL

SwissFEL will be a hard x-ray fourth generation light source to be built at Paul Scherrer Institut (PSI), Switzerland. In SwissFEL the electron bunches will be produced with a length of 3ps and will then be compressed by a factor of more than 1000 down to a few fs in order to generate ultra short x-ray pulses. Therefore reliable, accurate and noninvasive longitudinal diagnostic is essential after each compressing stage. In order to meet the requirements of this machine, new monitors have to be developed. We will present recent results of setups that measure electro-magnetic radiation, namely edge, synchrotron and diffraction radiation, emitted by the electron bunches (far field, spectral domain). These monitors are tested in the SwissFEL Injector Test Facility. A state of the art S-band Transverse Deflecting Cavity together with a Screen Monitor is used for calibration

Mapping 3D networks in human lung tissue using micro-computed tomography and immunofluorescence

Micro-computed tomography (µCT) is a non-destructive imaging technique that can reveal the 3D lung microstructure. 3D networks in µCT images are generally identified and segmented by manually tracing their outline, which is very time consuming and requires specialist knowledge of the tissue. We devised a new method to segment 3D networks and specific cell types semi-automatically by correlating µCT imaging with immunofluorescence microscopy. Using a prototype µCT system optimised for unstained soft tissues (Nikon Metrology, UK) we imaged unstained formalin-fixed paraffin-embedded human lung tissue at a voxel (3D pixel) size of 6-10 µm. The tissue was then sectioned and specific immunofluorescence staining performed at 20 µm intervals with primary antibodies for CK18 (airway epithelium) and CD68 (macrophages). Fluorescence microscopy images were digitised and registered to the µCT data. The blood vessel network was semi-automatically segmented using the µCT data and a region growing tool in the open source itk-SNAP software package (http://www.itksnap.org). Immunofluorescence staining was successfully distinguished from the background autofluorescence on paraffin-embedded lung tissue by using a far-red (>650 nm) emission secondary antibody. The autofluorescence was used to align the two-dimensional (2D) fluorescence microscopy to the three-dimensional (3D) µCT images using the BigWarp plugin in ImageJ (https://imagej.net/BigWarp). The aligned immunofluorescence images indicated the specific location of airway epithelium in the 3D lung volume and were used to semi-automatically segment the networks and cells in the µCT. Gaps in the 3D network between the immunofluorescently stained sections were filled by digital interpolation guided by the µCT data using itk-SNAP. The segmented 3D network of blood vessels and airways can then be further related to the location of immune cells (macrophages). In summary, correlation of 2D immunofluorescence and 3D µCT data permits localisation and segmentation of 3D lung networks and individual cell types in fixed human lung tissue. This novel correlative workflow allows for accurate, specific, and faster 3D network segmentation of human soft tissue

Dataset for X-ray micro-computed tomography for non-destructive 3D X-ray histology

Datasets used for the study entitled &#39;X-ray micro-computed tomography for non-destructive 3D X-ray histology&#39; byOrestis L. Katsamenis, Michael Olding, Jane A. Warner, David S. Chatelet, Mark G. Jones, Giacomo Sgalla, Bennie Smit, Oliver J. Larkin, Ian Haig, Luca Richeldi, Ian Sinclair, Peter M. Lackie, Philipp Schneider. The American Journal of PathologyAbstract for the paper Historically, micro-computed tomography has been considered unsuitable for histological analysis of unstained formalin-fixed and paraffin-embedded (FFPE) soft tissue biopsies due to a lack of image contrast between the tissue and the paraffin. However, we recently demonstrated that &mu;CT can successfully resolve microstructural detail in routinely prepared tissue specimens. Here, we illustrate how &mu;CT imaging of standard FFPE biopsies can be seamlessly integrated into conventional histology workflows, enabling non-destructive three-dimensional (3D) X-ray histology, the use and benefits of which we showcase for the exemplar of human lung biopsy specimens. This technology advancement was achieved through manufacturing a first-of-kind &mu;CT scanner for X-ray histology and developing optimised imaging protocols, which do not require any additional sample preparation. 3D X-ray histology allows for non-destructive 3D imaging of tissue microstructure, resolving structural connectivity and heterogeneity of complex tissue networks, such as the vascular or the respiratory tract. We also demonstrate that 3D X-ray histology can yield consistent and reproducible image quality, enabling quantitative assessment of tissue&rsquo;s 3D microstructures, which is inaccessible to conventional two-dimensional histology. Being non-destructive the technique does not interfere with histology workflows, permitting subsequent tissue characterisation by means of conventional light microscopy-based histology, immunohistochemistry, and immunofluorescence. 3D X-ray histology can be readily applied to a plethora of archival materials, yielding unprecedented opportunities in diagnosis and research of disease.</span

X-ray micro-computed tomography for nondestructive three-dimensional (3D) x-ray histology

Historically, micro-computed tomography (μCT) has been considered unsuitable for histologic analysis of unstained formalin-fixed, paraffin-embedded soft tissue biopsy specimens because of a lack of image contrast between the tissue and the paraffin. However, we recently demonstrated that μCT can successfully resolve microstructural detail in routinely prepared tissue specimens. Herein, we illustrate how μCT imaging of standard formalin-fixed, paraffin-embedded biopsy specimens can be seamlessly integrated into conventional histology workflows, enabling nondestructive three-dimensional (3D) X-ray histology, the use and benefits of which we showcase for the exemplar of human lung biopsy specimens. This technology advancement was achieved through manufacturing a first-of-kind μCT scanner for X-ray histology and developing optimized imaging protocols, which do not require any additional sample preparation. 3D X-ray histology allows for nondestructive 3D imaging of tissue microstructure, resolving structural connectivity and heterogeneity of complex tissue networks, such as the vascular network or the respiratory tract. We also demonstrate that 3D X-ray histology can yield consistent and reproducible image quality, enabling quantitative assessment of a tissue's 3D microstructures, which is inaccessible to conventional two-dimensional histology. Being nondestructive, the technique does not interfere with histology workflows, permitting subsequent tissue characterization by means of conventional light microscopy-based histology, immunohistochemistry, and immunofluorescence. 3D X-ray histology can be readily applied to a plethora of archival materials, yielding unprecedented opportunities in diagnosis and research of disease.</p

Biogeography of time partitioning in mammals.

notes: PMCID: PMC4183310types: Journal Article; Research Support, Non-U.S. Gov'tCopyright © 2014 National Academy of Sciences.This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1216063110/-/DCSupplemental.This is the post print version of the article accepted in PNAS.Many animals regulate their activity over a 24-h sleep-wake cycle, concentrating their peak periods of activity to coincide with the hours of daylight, darkness, or twilight, or using different periods of light and darkness in more complex ways. These behavioral differences, which are in themselves functional traits, are associated with suites of physiological and morphological adaptations with implications for the ecological roles of species. The biogeography of diel time partitioning is, however, poorly understood. Here, we document basic biogeographic patterns of time partitioning by mammals and ecologically relevant large-scale patterns of natural variation in "illuminated activity time" constrained by temperature, and we determine how well the first of these are predicted by the second. Although the majority of mammals are nocturnal, the distributions of diurnal and crepuscular species richness are strongly associated with the availability of biologically useful daylight and twilight, respectively. Cathemerality is associated with relatively long hours of daylight and twilight in the northern Holarctic region, whereas the proportion of nocturnal species is highest in arid regions and lowest at extreme high altitudes. Although thermal constraints on activity have been identified as key to the distributions of organisms, constraints due to functional adaptation to the light environment are less well studied. Global patterns in diversity are constrained by the availability of the temporal niche; disruption of these constraints by the spread of artificial lighting and anthropogenic climate change, and the potential effects on time partitioning, are likely to be critical influences on species' future distributions.ER