Mineral Separate Microanalysis with Intelligent Spot Placement, Manual Edition, and Simulation: Two Correlative Microscopy Prototypes for Relating Zircon Texture, Age, and Geochemistry

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Mineral Separate Microanalysis with Intelligent Spot Placement, Manual Edition, and Simulation: Two Correlative Microscopy Prototypes for Relating Zircon Texture, Age, and Geochemistry

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Author(s): Marco A. Acevedo Zamora ¹ ^, , John T. Caulfield ¹ , Elise Laupland ¹ , Balz S. Kamber ¹ , Charlotte M. Allen ¹

Publication date (Electronic): 21 January 2025

Conference name: 13th Asia Pacific Microscopy Congress 2025 (APMC13)

Conference date: 2-7 Febuary 2025

Keywords: Correlative microscopy, Image analysis, QuPath, LA-ICP-MS spots, SEM cathodoluminescence

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Abstract

The study of mineral separates for petrogenesis, geochronology, and exploration requires the use of microscopy imaging techniques including optical stereomicroscopy, petrographic microscopy, electron microscopy (SEM), and microanalytical spectrometry. Technicians and scientists have a large set of digital tools available in each acquisition system to assist in acquisition, data processing, management, data reduction, and preliminary image analysis. The next generation of geoscientific studies and software requires increasing the automation potential, combining and integrating microscopic techniques across the board to achieve maximum insight ^{[ 1]}. The integration requires deploying whole-slide imaging and image registration to establish a common data space, making the approach increasingly attractive to the broader geoscientific community.

Bioinformatics and geospatial sciences have already crossed the learning barrier frontiers of the digital era. This was possible thanks to revolutionary software configuring image analysis pipelines (e.g., ImageJ-Fiji ^{[ 2]}, eCognition ^{[ 3]}, OrfeoToolbox ^{[ 4]}) that facilitated the connection of data streams from different instruments (microscopes) or detection systems (satellites) to enable online (e.g., CATMAID ^{[ 5]}, Cytomine ^{[ 6]}) and offline (e.g., QuPath ^{[ 7]}, QGIS) multi-disciplinary research on multi-gigapixel images.

This presentation will showcase two pipeline prototypes for correlative microscopy that allow end-users to interact with high-level information derived from individual mineral grains (registered, segmented, and classified) and place virtual microanalytical spots. The pipelines allow manual addition of editable spots (prototype 1 in Figure 1) and/or fully automated simulation (new algorithm) of spot locations (prototype 2 in Figure 2). The virtual spots can be transferred to the laser ablation system software for running consecutive, lengthy analytical sessions comprising many 100s of analytical spots with minimal time investment.

Fig. 1

Zircon mount opened in QuPath software showing grains in SEM cathodoluminescence and candidate microanalytical spot locations. A panel (points) has been opened listing points that the user can manually edit to plan the experiment. The same spots are latter transferred to the laser system software using a multi-step image registration. The scale is 200 px (bottom left of canvas).

Fig. 2

Zircon mount showing the simulation of microanalytical spots (black circles) placed on a segmented cathodoluminescence image (top: overview; bottom: closeup). The segmented image input is shown with random colors for enhancing visibility. The spots were placed by a new algorithm (no user input). The scale of the image is 1 micron/px and the markers are at the field of view frame.

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Publication date (Electronic): 21 January 2025

Electronic Location Identifier: e280

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[1 ]Queensland University of Technology, School of Earth and Atmospheric Sciences, Brisbane, QLD, Australia

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*Corresponding author: marco.acevedozamora@ 123456qut.edu.au

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Marco A. Acevedo Zamora https://orcid.org/0000-0003-3330-3828

Article

DOI: 10.14293/APMC13-2025-0280

SO-VID: 2f85e6d5-c683-4baf-8df0-b4d500a43fc4

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Published under Creative Commons Attribution 4.0 International ( CC BY 4.0). Users are allowed to share (copy and redistribute the material in any medium or format) and adapt (remix, transform, and build upon the material for any purpose, even commercially), as long as the authors and the publisher are explicitly identified and properly acknowledged as the original source.

Conference name: 13th Asia Pacific Microscopy Congress 2025

Conference acronym: APMC13

Conference number: 13

Conference location: Brisbane, Australia

Conference date: 2-7 Febuary 2025

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Funding

The authors acknowledge funding from BHP given to Queensland University of Technology. Data reported in this abstract were obtained at the Central Analytical Research Facility (CARF) at QUT.

References

Acevedo Zamora, M. Thesis by publication, Queensland University of Technology (2024). Brisbane. https://eprints.qut.edu.au/248815/
Bankhead, P., Loughrey, M. B., Fernandez, J. A., Dombrowski, Y., McArt, D. G., Dunne, P. D., McQuaid, S., Gray, R. T., Murray, L. J., Coleman, H. G., James, J. A., Salto-Tellez, M., & Hamilton, P. W. Sci Rep, 7(1), 16878 (2017). https://doi.org/10.1038/s41598-017-17204-5
Grizonnet, M., Michel, J., Poughon, V., Inglada, J., Savinaud, M., & Cresson, R. Open Geospatial Data, Software and Standards, 2(1), 15 (2017). https://doi.org/10.1186/s40965-017-0031-6
Marée, R., Rollus, L., Stevens, B., Hoyoux, R., Louppe, G., Vandaele, R., Begon, J.-M., Kainz, P., Geurts, P., & Wehenkel, L. Bioinformatics, 32(9), 1395-1401 (2016). https://doi.org/10.1093/bioinformatics/btw013
Nussbaum, S., & Menz, G. in “Object-Based Image Analysis and Treaty Verification: New Approaches in Remote Sensing – Applied to Nuclear Facilities in Iran (pp. 29-39)”, S. Nussbaum & G. Menz (Eds.). Springer Netherlands (2008). https://doi.org/10.1007/978-1-4020-6961-1_3
Saalfeld, S., Cardona, A., Hartenstein, V., & Tomančák, P. Bioinformatics, 25(15), 1984-1986 (2009). https://doi.org/10.1093/bioinformatics/btp266
Schindelin, J., Arganda-Carreras, I., Frise, E., Kaynig, V., Longair, M., Pietzsch, T., Preibisch, S., Rueden, C., Saalfeld, S., Schmid, B., Tinevez, J. Y., White, D. J., Hartenstein, V., Eliceiri, K., Tomancak, P., & Cardona, A. Nat Methods, 9(7), 676-682 (2012). https://doi.org/10.1038/nmeth.2019

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[1] Acevedo Zamora, M. Thesis by publication, Queensland University of Technology (2024). Brisbane. https://eprints.qut.edu.au/248815/

[2] Bankhead, P., Loughrey, M. B., Fernandez, J. A., Dombrowski, Y., McArt, D. G., Dunne, P. D., McQuaid, S., Gray, R. T., Murray, L. J., Coleman, H. G., James, J. A., Salto-Tellez, M., & Hamilton, P. W. Sci Rep, 7(1), 16878 (2017). https://doi.org/10.1038/s41598-017-17204-5

[3] Grizonnet, M., Michel, J., Poughon, V., Inglada, J., Savinaud, M., & Cresson, R. Open Geospatial Data, Software and Standards, 2(1), 15 (2017). https://doi.org/10.1186/s40965-017-0031-6

[4] Marée, R., Rollus, L., Stevens, B., Hoyoux, R., Louppe, G., Vandaele, R., Begon, J.-M., Kainz, P., Geurts, P., & Wehenkel, L. Bioinformatics, 32(9), 1395-1401 (2016). https://doi.org/10.1093/bioinformatics/btw013

[5] Nussbaum, S., & Menz, G. in “Object-Based Image Analysis and Treaty Verification: New Approaches in Remote Sensing – Applied to Nuclear Facilities in Iran (pp. 29-39)”, S. Nussbaum & G. Menz (Eds.). Springer Netherlands (2008). https://doi.org/10.1007/978-1-4020-6961-1_3

[6] Saalfeld, S., Cardona, A., Hartenstein, V., & Tomančák, P. Bioinformatics, 25(15), 1984-1986 (2009). https://doi.org/10.1093/bioinformatics/btp266

[7] Schindelin, J., Arganda-Carreras, I., Frise, E., Kaynig, V., Longair, M., Pietzsch, T., Preibisch, S., Rueden, C., Saalfeld, S., Schmid, B., Tinevez, J. Y., White, D. J., Hartenstein, V., Eliceiri, K., Tomancak, P., & Cardona, A. Nat Methods, 9(7), 676-682 (2012). https://doi.org/10.1038/nmeth.2019

Mineral Separate Microanalysis with Intelligent Spot Placement, Manual Edition, and Simulation: Two Correlative Microscopy Prototypes for Relating Zircon Texture, Age, and Geochemistry

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