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Quantifying the Structure and Composition of Flocculated Suspended Particulate Matter Using Focused Ion Beam Nanotomography Jonathan A.T. Wheatland, Andrew J. Bushby, and Kate L. Spencer Environ. Sci. Technol., Just Accepted Manuscript • DOI: 10.1021/acs.est.7b00770 • Publication Date (Web): 10 Jul 2017 Downloaded from http://pubs.acs.org on July 10, 2017
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Length-scales over which the imaging techniques commonly used to characterise floc properties operate, with corresponding typical cross-section (XY) and resolution achieved by each technique. FIB-nt is shown and can be seen to fill the observational gap between traditional 2D COM and video camera systems at the gross-scale and (S)TEM at the nano-scale. 84x109mm (300 x 300 DPI)
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Microscope set-up for FIB-nt: (a) Simplified graphic of a dual beam FIB-SEM showing the orientation of the ion and electron beams; (b) Standard geometry of sample within FIB-SEM chamber for ion milling and FIBnt (adapted from Holzer et al.29); (c) Example of a volume (S3-SE) prepared for FIB-nt; the sample is oriented at an oblique angle relative to the electron beam as shown in (b). 82x80mm (300 x 300 DPI)
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Dark-field STEM images showing; (a-b) Clay minerals (cm), bacterial cells (ba) and organic membranes (om); (b) Magnified sub-set of (a) showing the internal structure of a bacteria and surrounding EPS filling the pore space between the cell and surrounding clay minerals (contrast inverted); (c) Cyanobacterium surround by clay minerals. 53x110mm (300 x 300 DPI)
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SEM images of FIB-milled cross-section generated using (a) SEs and (b) BSEs; sub-sets isolating a cluster of inorganic particles (c) and a bacterium (d). The dashed lines in (c) and (d) indicate the position of the adjacent grey-scale line profiles shown in (e) and (f), which demonstrate the difference in contrast and resolution between the two detection methods applied here. 148x101mm (300 x 300 DPI)
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Feature segmentation of SEM images; (a) Original SE image; (b–d ) Binary masks achieved by histogram based thresholding; (e) Screenshot of the TWS tool window showing the segmentation procedure; (f) Binary mask achieved using the TWS plugin; (g) Table showing the number of objects counted and the %.Vol. of occupied pixels for the different threshold values (b–d ) and Weka segmentation (f); (h–j) 3D reconstruction of the clay particle-particle association identified in sub-volume obtained from S3-SE (see Figure 6a). 159x139mm (300 x 300 DPI)
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3D reconstructions of FIB-nt volume S3-SE based on SE images; (a) Segmented components and the location of the magnified sub-volume depicted in Figure 6; (b) Same as (a) but clay have been rendered transparent to reveal the bacteria and non-clay minerals; (c) Selected SE 2D image from the original image stack [location within the volume indicated by red line shown in (b)] showing larger micro-scale ‘channels’ and nano-scale pore space; (d) Binary mask of (c) generated by TWS. 122x130mm (300 x 300 DPI)
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3D reconstructions of volume S3-BSE based on BSE images: (a) Segmented components identified within the analysed volume; (b) Same as (a) but clay minerals rendered transparent to reveal organic components; (c) Isolated cyanobacterium with cell wall rendered transparent; (d) Selected BSE image from original image stack [location identified in (c)] showing the ultrastructure of the cyanobacterium; (e) Segmented subcomponents of the cyanobacterial cell. 177x144mm (300 x 300 DPI)
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Quantifying the Structure and Composition of Flocculated Suspended Particulate
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Matter Using Focused Ion Beam Nanotomography
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Jonathan A.T. Wheatland,*,†,§,‡ Andrew J. Bushby,†,§ Kate L. Spencer‡
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†
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Road, London E1 4NS, UK.
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§
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4NS, UK.
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‡
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UK.
School of Engineering & Materials Science, Queen Mary University of London, Mile End
The NanoVision Centre, Queen Mary University of London, Mile End Road, London E1
School of Geography, Queen Mary University of London, Mile End Road, London E1 4NS,
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* Corresponding author. Email addresses:
[email protected]; phone: +44 (0)20
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7882 2717.
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ABSTRACT
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Suspended particulate matter (SPM) is present in the natural aquatic environment as loosely
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bound aggregates or ‘flocs’ and is responsible for the transport and fate of sediment, carbon,
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nutrients, pollutants, pathogens and manufactured nanoparticles from catchment to coast.
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Accurate prediction of SPM hydrodynamics requires the quantification of 3D floc properties
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(size, shape, density and porosity) that span several spatial scales. Yet, current techniques
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(video camera systems, optical microscopy and transmission electron microscopy, TEM) can
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only provide 2D simplifications of size and shape with a spatial resolution gap between the
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‘gross’ (>100s µm) and nano-scale (
