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Electron and X-ray microscopy Community for structural and chemical Imaging Techniques for Earth materials

Deliverables

Delivery of 6 days of access to installation 1 (macro-CT) at TUD
Report on market consultation to identify IT infrastructures
Report on the organization of training workshops
Delivery of 36 days of access to installation 2 (QEMSCAN) at CAM
Final Report

Final Report to assess the success of EXCITE

Delivery of 62 days of access to installation 2 (X-ray μ-CT) at UGR
Report on outreach activities to new users [1]

Report on outreach activities to new users in the first 12 months of the project

Delivery of 384 hours of access to installation 2 (EPMA) at FCUL
Documentation and analysis of EXCITE workflows

Report on documentation and analysis of EXCITE workflows We will compare workflows and identify how to standardise the reporting of the procedures and the steps that are needed for different research needs and applications

Delivery of 53 days of access to installation 3 (WEMS) at CAM
Communication and dissemination plan

A communication and dissemination plan will be made to ensure effective communication channels

Delivery of 410 days of access to EM Centre at UU
Report on the demands of the user community
Delivery of 8 days of access to installation 1 (micro-CT) at UEDIN
Report on developing and implementing quantitative density imaging from X-ray absorption scans

Report on developing and implementing quantitative density imaging from Xray absorption scans

Report on conferences and meetings with EXCITE representation [2]

Report on conferences and meetings with EXCITE representation in M19-36

Delivery of 336 hours of access to installation 2 (High Speed Tomography) at UPPA
Delivery of 384 hours of access to installation 1 (High Resolution Tomography) at UPPA
Report on TA evaluation and TA delivery in 2nd call
Delivery of 253 hours of access to installation 1 (EPMA) at LNEG
Report on community-driven, open-source solution for correlative microscopy

Report on communitydriven opensource solution for correlative microscopy

Delivery of 30 days of access to installation 1 (Tomografi) at NTNU
Results and comparison of analyses of reference samples including recommendations on the use of reference samples in X-ray imaging applications

Report on results and comparison of analyses of reference samples including recommendations on the use of reference samples in X-ray imaging applications

Report on the application of hyperspectral imaging for automated mineralogy
Report on workflow development of combining automated secondary and backscattered electron imaging with automated EDX mapping, cathodoluminescence imaging and EBSD
Report on outreach activities to new users [2]

Report on outreach activities to new users in M12-36

Best practice recommendations for platform- specific EXCITE workflows

We will develop best-practice guidelines for platform-specific workflows for different scientific applications. In addition to addressing workflow steps directly related to sample preparation and data collection, guidelines will include recommendations for data management and processing based on the outcome of networking Task 4.1 (data standardisation and management across EXCITE).

Report on combining SEM imaging with spatially correlated TEM preparation and 4D STEM
Delivery of 65 days of access to installation 1 (Electron Microprobe) at CAM
Sustainability plan for trans-national access beyond EXCITE

The sustainability plan for trans-national access beyond EXCITE which will be report containging an evaluation of significant funding opportunities that will help sustain, entirely or in part, the access facilities or the future research infrastructure. Included in this will be fact-finding from national, commercial and EU funders, including shared funding schemes and identification of any barriers for users or funders that might prevent specific funding being made available for access activities. Resulting from this we will propose an Engagement Plan which will suggest ways of engaging with funders at various levels and scope the growth potential available outside of the EU, to identify sources for new funding associated with a global user community or specially themed global research programmes. Finally, we will evaluate possibilities to stimulate spinoff companies and SMEs to commercially use the infrastructures, where possible in coordination with national and regional efforts.

Progress report

Progress report to assess the success of EXCITE

Delivery of 42 days of access to installation 2 (X-ray micro-CT) at OV
Delivery of 49 days of access to installation 1 (HRTEM) at UGR
Report on the application of deep learning and multi-modal segmentation of X-ray tomography data
Delivery of 15 days of access to installation 2 (Radiografi) at NTNU
Delivery of 94 days of access to installation 1 (FESEM/EMPA) at RM1
Foresight White Paper for EXCITE TNA

Foresight White Paper for EXCITE TNA in which we explore which funding schemes and access modes can assure sustainability of EXCITE TNA in particular and earthmaterials microscopy in general

Report on collaborations with existing ESFRI and other world-class RIs

Report on collaborations with existing ESFRI and other worldclass RIs

Report on uniting X-ray and electron microscopy
Delivery of 43 days of access to CrystalProbe- Montpellier at CNRS
Management guidelines
Delivery of 30 days of access to installation 2 (SEM) at UiO
Delivery of 62 days of access to installation 2 (micro-CT) at TUD
Delivery of 17 days of access to installation 1 (Micro/Nano-CT) at UiO
Results and comparison of analyses of reference samples including recommendations on the use of reference samples in electron imaging applications

Report on results and comparison of analyses of reference samples including recommendations on the use of reference samples in electron imaging applications

Report on identifying future perspectives in incorporating a broader spectrum of imaging probes
Report on the organization of annual user meetings
Report on the development of Virtual Desktop Infrastructure
Midterm summary report on networking activities
Delivery of 253 days of access to UGCT at UGent
Report on TA evaluation and TA delivery in 1st call
Delivery of 213 days of access to PISA at GFZ
Report on conferences and meetings with EXCITE representation [1]

Report on conferences and meetings with EXCITE representation in M118

Report on the application of smart scanning and ML image reconstruction/in-painting algorithms to accelerate data acquisition and processing
Delivery of 55 days of access to HIF Sp-CT at HZDR
Report on combining data from absorption CT and μXRF
Initial data management plan

Creating an Initial data management plan This initial Data Management Plan describes the existing and planned data management data access and data security policies

Publications

The Influence of Undercooling and Sector Zoning on Clinopyroxene–Melt Equilibrium and Thermobarometry

Author(s): Alice MacDonald, Teresa Ubide, Silvio Mollo, Alessio Pontesilli, Matteo Masotta
Published in: Journal of Petrology, Issue 64(10), 2023, ISSN 0022-3530
Publisher: Oxford University Press
DOI: 10.1093/petrology/egad074

Protracted localization of metamorphism and deformation in a heterogeneous lower-crustal shear zone

Author(s): Sascha Zertani, Luca Menegon, Giorgio Pennacchioni, Iris Buisman, Fernando Corfu, Bjørn Jamtveit
Published in: Journal of Structural Geology, Issue 176, 2023, ISSN 0191-8141
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.jsg.2023.104960

The effect of aqueous fluid on viscous relaxation of garnet and modification of inclusion pressures after entrapment

Author(s): Xin Zhong, David Wallis, Phillip Kingsbery, Timm John
Published in: Earth and Planetary Science Letters, Issue 636, 2024, ISSN 0012-821X
Publisher: Elsevier BV
DOI: 10.1016/j.epsl.2024.118713

Combining Automated Mineralogy with X-ray Computed Tomography for Internal Characterization of Ore Samples at the Microscopic Scale

Author(s): Florian Buyse, Stijn Dewaele, Matthieu N. Boone & Veerle Cnudde
Published in: Natural Resources Research, Issue 32, 2023, Page(s) 461-478, ISSN 1573-8981
Publisher: Springer
DOI: 10.1007/s11053-023-10161-z

On-fault earthquake energy density partitioning from shocked garnet in an exhumed seismic midcrustal fault

Author(s): Giovanni Toffol, Giorgio Pennacchioni, Luca Menegon, David Wallis, Manuele Faccenda, Alfredo Camacho, Michel Bestmann
Published in: Science Advances, Issue 10 - 9, 2024, ISSN 2375-2548
Publisher: American Association for the Advancement of Science
DOI: 10.1126/sciadv.adi8533

Beyond the surface: Coupling water permeability assessments to X-ray micro-computed tomography for evaluation of self-healing on lime-based mortars

Author(s): Grosso Giordano F.; Valdez Madrid D.; Schröer L.; Boon N.; Cnudde V.; De Belie N.
Published in: Construction and Building Materials, Issue 431, 2024, ISSN 0950-0618
Publisher: Elsevier BV
DOI: 10.1016/j.conbuildmat.2024.136603

Magnetic and microscopic investigation of airborne iron oxide nanoparticles in the London Underground

Author(s): H. A. Sheikh, P. Y. Tung, E. Ringe & R. J. Harrison
Published in: Scientific Reports, Issue 12, 2022, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-022-24679-4

3D Visualization of cyanobacterial biofilms using micro-computed tomography with contrast-enhancing staining agents

Author(s): Laurenz Schröer, Tim Balcaen, Karel Folens, Nico Boon, Tim De Kock, Greet Kerckhofs, Veerle Cnudde
Published in: Tomography of Materials and Structures, Issue 4, 2024, ISSN 2949-673X
Publisher: Elsevier BV
DOI: 10.1016/j.tmater.2024.100024

Micro computed tomography images of capillary actions in rough and irregular granular materials

Author(s): Nadimi S.; Mendes J.; López A.; Schröer L.; Manoorkar S.; Ellman S.; Cnudde V.; Bruno A.W.
Published in: Scientific Data, Issue 11-1-78, 2024, ISSN 2052-4463
Publisher: Nature Research
DOI: 10.1038/s41597-024-02925-w

SIGMA: Spectral Interpretation using Gaussian Mixtures and Autoencoder

Author(s): Po-Yen Tung, Hassan Aftab Sheikh, Matthew R Ball, Farhang Nabiei, and Richard Harrison
Published in: Geochemistry, Geophysics, Geosystems, Issue 24(1), 2023, Page(s) online, ISSN 1525-2027
Publisher: Geochemical Society
DOI: 10.1029/2022gc010530

Microstructural and isotopic analysis of shocked monazite from the Hiawatha impact structure: development of porosity and its utility in dating impact craters

Author(s): Hyde W.R.; Kenny G.G.; Whitehouse M.J.; Wirth R.; Roddatis V.; Schreiber A.; Garde A.A.; Plan A.; Larsen N.K.
Published in: Contributions to Mineralogy and Petrology, Issue 179-3, 2024, ISSN 0010-7999
Publisher: Springer Verlag
DOI: 10.1007/s00410-024-02097-1

Adhesion evaluation and interface characterization of 3D printed concrete for automatic repair

Author(s): Yaxin Tao a, Yi Zhang a b, Xiaoyun Wang a c, Jose R.A. Godinho d, Geert De Schutter a, Kim Van Tittelboom a
Published in: Construction and Building Materials, Issue 414, 2024, ISSN 0950-0618
Publisher: Elsevier BV
DOI: 10.1016/j.conbuildmat.2024.134952

Sulfide Melt Wetting Properties in Earth's Mantle: New Constraints From Combined 2D and 3D Imaging

Author(s): Beyer C.; Fonseca R.O.C.; Bissbort T.; Schröer L.; Cnudde V.
Published in: Geochemistry, Geophysics, Geosystems, Issue 2505, 2024, ISSN 1525-2027
Publisher: Geochemical Society
DOI: 10.1029/2024gc011535

Hydrothermal alteration of accessory minerals (allanite and titanite) in the late Archean Closepet granitoid (Dharwar Craton, India): A TEM study

Author(s): Gmochowska W.; Wirth R.; Słaby E.; Anczkiewicz R.; Krzątała A.; Roddatis V.; Sláma J.; Kozub-Budzyń G.A.; Bhattacharya S.; Schreiber A.
Published in: Geochemistry, 2024, ISSN 0009-2819
Publisher: Gustav Fischer Verlag
DOI: 10.1016/j.chemer.2024.126130

Contribution of 3D automated mineralogy in unraveling the formation history of Nb-Ta-Sn mineralized LCT pegmatites in the Karagwe-Ankole belt (Central Africa)

Author(s): Florian BUYSE, Stijn DEWAELE, Matthieu N. BOONE & Veerle CNUDDE
Published in: Geologica Belgica, Issue 27(1-2), 2024, ISSN 1374-8505
Publisher: Geologica Belgica
DOI: 10.20341/gb.2024.001

Quantifying frost-weathering-induced damage in alpine rocks

Author(s): Mayer, Till; Deprez, Maxim; Schröer, Laurenz; Cnudde, Veerle; Draebing, Daniel
Published in: Cryosphere, Issue Volume 18, Issue 6, 2024, Page(s) 2847-2864, ISSN 1994-0416
Publisher: Copernicus Group
DOI: 10.5194/tc-18-2847-2024

Influence of different sample preparation techniques on imaging viruses and virus-like particles by scanning electron and scanning transmission electron microscopes

Author(s): Monika Kąkol, Ezher Tagliasacchi, Andrzej Borkowski, Mirosław Słowakiewicz
Published in: Frontiers in Microbiology, Issue 14, 2023, Page(s) online, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2023.1279720

The Impact of Grain-Size Distributions of Iron-Oxides on Paleomagnetic Measurements

Author(s): Out F.; de Boer R.A.; Walmsley J.; de Groot L.V.
Published in: Geochemistry, Geophysics, Geosystems, Issue 25-4, 2024, ISSN 1525-2027
Publisher: Geochemical Society
DOI: 10.1029/2024gc011512

REE Concentrations in Secondary Uranium Minerals from the Izera Metamorphic Complex (SW Poland)

Author(s): Marcin Daniel Syczewski, Rafał Siuda, Jan Parafiniuk
Published in: Minerals, Issue 13(7), 2023, ISSN 2075-163X
Publisher: MDPI
DOI: 10.3390/min13070945

Geochemical behavior of heavy metals and radionuclides in a pit lake affected by acid mine drainage (AMD) in the Muskau Arch (Poland)

Author(s): Sekudewicz I.; Syczewski M.; Rohovec J.; Matouskova; Kowalewska U.; Blukis R.; Geibert W.; Stimac I.; Gąsiorowski M.
Published in: Science of the Total Environment, Issue 908, 2024, ISSN 0048-9697
Publisher: Elsevier BV
DOI: 10.1016/j.scitotenv.2023.168245

Increasing control over biomineralization in conodont evolution

Author(s): Bryan Shirley, Isabella Leonhard, Duncan J. E. Murdock, John Repetski, Przemysław Świś, Michel Bestmann, Pat Trimby, Markus Ohl, Oliver Plümper, Helen E. King & Emilia Jarochowska
Published in: Nature Communications, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-024-49526-0

Non-destructive evaluation of ductile-porous versus brittle 3D printed vascular networks in self-healing concrete

Author(s): Yasmina Shields, Eleni Tsangouri, Claire Riordan, Cristina De Nardi, Jose Ricardo Assunção Godinho, Ticho Ooms, Paola Antonaci, Dave Palmer, Abir Al-Tabbaa, Tony Jefferson, Nele De Belie, Kim Van Tittelboom,
Published in: Cement and Concrete Composites, Issue 145, 2024, ISSN 0958-9465
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.cemconcomp.2023.105333

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