What Lies Beneath: 3D vs 2D Correlative Imaging Challenges and How to Overcome Them

Mitchell, Ria L.; Freitag, Stefanie; Volkenandt, Tobias; Russell, James E.; Davies, Peter; Pleydell‐Pearce, Cameron; Johnston, Richard

doi:10.1017/s1431927619002812

Cited by 5 publications

(9 citation statements)

References 3 publications

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“…In this step, a ‘targeted slice’ was chosen from the XRM data, and from that a known amount of sample surface material (measured using the XRM scan images) can be removed. This is achieved via grinding and polishing of the sample surface 73 , and in our case, 574 µm (Fig. 3 ) needed to be removed to expose the targeted region.…”

Section: Methodsmentioning

confidence: 99%

“…The resin block was frequently measured using a Hilka digital calliper to ensure the correct thickness of sample was removed. Further details on this manual correlative sample preparation method can be found in 73 . Our results were within 20 µm of the targeted slice (i.e., 554 µm was removed), so a new XRM slice was chosen for the following image correlation to match the newly exposed surface (Fig.…”

Section: Methodsmentioning

confidence: 99%

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Correlative Microscopy: a tool for understanding soil weathering in modern analogues of early terrestrial biospheres

Mitchell

Davies

Kenrick

et al. 2021

Sci Rep

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Correlative imaging provides a method of investigating complex systems by combining analytical (chemistry) and imaging (tomography) information across dimensions (2D-3D) and scales (centimetres-nanometres). We studied weathering processes in a modern cryptogamic ground cover from Iceland, containing early colonizing, and evolutionary ancient, communities of mosses, lichens, fungi, and bacteria. Targeted multi-scale X-ray Microscopy of a grain in-situ within a soil core revealed networks of surficial and internal features (tunnels) originating from organic-rich surface holes. Further targeted 2D grain characterisation by optical microscopy (OM), scanning electron microscopy (SEM), and energy dispersive X-ray spectroscopy (SEM–EDS), following an intermediate manual correlative preparation step, revealed Fe-rich nodules within the tunnels. Finally, nanotomographic imaging by focussed ion beam microscopy (FIB-SEM) revealed coccoid and filamentous-like structures within subsurface tunnels, as well as accumulations of Fe and S in grain surface crusts, which may represent a biological rock varnish/glaze. We attribute these features to biological processes. This work highlights the advantages and novelty of the correlative imaging approach, across scales, dimensions, and modes, to investigate biological weathering processes. Further, we demonstrate correlative microscopy as a means of identifying fingerprints of biological communities, which could be used in the geologic rock record and on extra-terrestrial bodies.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Correlative Microscopy: a tool for understanding soil weathering in modern analogues of early terrestrial biospheres

Mitchell

Davies

Kenrick

et al. 2021

Sci Rep

View full text Add to dashboard Cite

show abstract

“…In this step, a 'targeted slice' was chosen from the XRM data, and from that a known amount of sample surface material (measured using the XRM scan images) can be removed. This is achieved via grinding and polishing of the sample surface 68 , and in our case, 574 µm (Fig. 3) needed to be removed to expose the targeted region.…”

Section: -Intermediate Correlative Microscopy Sample Preparation Stepmentioning

confidence: 99%

“…The resin block was frequently measured using a Hilka digital calliper to ensure the correct thickness of sample was removed. Further details on this manual correlative sample preparation method can be found in 68 . Our results were within 20 µm of the targeted slice (i.e., 544µm was removed), so a new XRM slice was chosen for the following image correlation to match the newly exposed surface (Fig.…”

Section: -Intermediate Correlative Microscopy Sample Preparation Stepmentioning

confidence: 99%

Correlative Microscopy: a tool for understanding soil weathering in modern analogues of early terrestrial biospheres

Mitchell¹,

Davies²,

Kenrick³

et al. 2021

Preprint

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Correlative imaging provides a method of investigating complex systems by combining analytical (chemistry) and imaging (tomography) information across dimensions (2D-3D) and scales (centimetres-nanometres). We studied weathering processes in a modern cryptogamic ground cover (CGC) from Iceland, containing early colonizing, and evolutionary ancient, communities of mosses, lichens, fungi, and bacteria. Targeted multi-scale X-ray Microscopy (XRM) of a grain in-situ within a soil core revealed networks of surficial and internal features (tunnels) originating from organic-rich surface holes. Further targeted 2D grain characterisation by optical microscopy (OM), scanning electron microscopy (SEM), and energy dispersive X-ray spectroscopy (SEM-EDS), following an intermediate manual correlative preparation step, revealed Fe-rich nodules within the tunnels. Finally, nanotomographic imaging by focussed ion beam microscopy (FIB-SEM) revealed coccoid and filamentous-like structures within subsurface tunnels, as well as accumulations of Fe and S in grain surface crusts, which may represent a biological rock varnish/glaze. We attribute these features to biological processes. This work highlights the advantages and novelty of the correlative imaging approach, across scales, dimensions, and modes, to investigate biological weathering processes. Further, we demonstrate correlative microscopy as a means of identifying fingerprints of biological communities, which could be used in the geologic rock record and on extra-terrestrial bodies.

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“…Common issues with traditional approaches are either high initial investment into sophisticated, dedicated instruments or problematic image correlation due to data incompatibility (data formats, pixel count and size, etc.) between devices used [7]. LiteScope is equipped with Correlative Probe and Electron Microscopy (CPEM)™ technology that enables simultaneous data acquisition and correlation of multiple channels; for example, the material contrast given by SEM is merged with the 3D topography of surface features obtained by AFM, resulting in a 3D CPEM view (Figure 1).…”

Section: Introductionmentioning

confidence: 99%

AFM-in-SEM as a Tool for Comprehensive Sample Surface Analysis

Novotná¹,

Horak²,

Konečný

et al. 2020

Micros. Today

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What Lies Beneath: 3D vs 2D Correlative Imaging Challenges and How to Overcome Them

Cited by 5 publications

References 3 publications

Correlative Microscopy: a tool for understanding soil weathering in modern analogues of early terrestrial biospheres

Correlative Microscopy: a tool for understanding soil weathering in modern analogues of early terrestrial biospheres

Correlative Microscopy: a tool for understanding soil weathering in modern analogues of early terrestrial biospheres

AFM-in-SEM as a Tool for Comprehensive Sample Surface Analysis

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