Compressed AFM-IR hyperspectral nanoimaging
Autor(a) principal: | |
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Data de Publicação: | 2024 |
Outros Autores: | , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/10362/163239 |
Resumo: | Funding Information: We gratefully acknowledge fruitful discussions with Alexander Govyadinov. We acknowledge financial support by Deutsche Forschungsgemeinschaft (Grants EL 492/1-1, RU 420/13-1). Sofia Cortes was supported by Fundação para a Ciência e Tecnologia (FCT) for funds to GHTM (UID/04413/2020). Publisher Copyright: © 2023 The Author(s). Published by IOP Publishing Ltd. |
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oai:run.unl.pt:10362/163239 |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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7160 |
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Compressed AFM-IR hyperspectral nanoimagingAFM-IRhyperspectral nanoimagingLeishmania parasiteslow-rank matrix reconstructionInstrumentationEngineering (miscellaneous)Applied MathematicsSDG 3 - Good Health and Well-beingSDG 9 - Industry, Innovation, and InfrastructureFunding Information: We gratefully acknowledge fruitful discussions with Alexander Govyadinov. We acknowledge financial support by Deutsche Forschungsgemeinschaft (Grants EL 492/1-1, RU 420/13-1). Sofia Cortes was supported by Fundação para a Ciência e Tecnologia (FCT) for funds to GHTM (UID/04413/2020). Publisher Copyright: © 2023 The Author(s). Published by IOP Publishing Ltd.Infrared (IR) hyperspectral imaging is a powerful approach in the field of materials and life sciences. However, for the extension to modern sub-diffraction nanoimaging it still remains a highly inefficient technique, as it acquires data via inherent sequential schemes. Here, we introduce the mathematical technique of low-rank matrix reconstruction to the sub-diffraction scheme of atomic force microscopy-based infrared spectroscopy (AFM-IR), for efficient hyperspectral IR nanoimaging. To demonstrate its application potential, we chose the trypanosomatid unicellular parasites Leishmania species as a realistic target of biological importance. The mid-IR spectral fingerprint window covering the spectral range from 1300 to 1900 cm−1 was chosen and a distance between the data points of 220 nm was used for nanoimaging of single parasites. The method of k-means cluster analysis was used for extracting the chemically distinct spatial locations. Subsequently, we randomly selected only 10% of an originally gathered data cube of 134 (x) × 50 (y) × 148 (spectral) AFM-IR measurements and completed the full data set by low-rank matrix reconstruction. This approach shows agreement in the cluster regions between full and reconstructed data cubes. Furthermore, we show that the results of the low-rank reconstruction are superior compared to alternative interpolation techniques in terms of error-metrics, cluster quality, and spectral interpretation for various subsampling ratios. We conclude that by using low-rank matrix reconstruction the data acquisition time can be reduced from more than 14 h to 1-2 h. These findings can significantly boost the practical applicability of hyperspectral nanoimaging in both academic and industrial settings involving nano- and bio-materials.Vector borne diseases and pathogens (VBD)Global Health and Tropical Medicine (GHTM)Instituto de Higiene e Medicina Tropical (IHMT)RUNKästner, B.Marschall, M.Hornemann, A.Metzner, S.Patoka, P.Cortes, S.Wübbeler, G.Hoehl, A.Rühl, E.Elster, C.2024-02-08T00:17:13Z2024-012024-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article8application/pdfhttp://hdl.handle.net/10362/163239eng0957-0233PURE: 82852880https://doi.org/10.1088/1361-6501/acfc27info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2024-03-11T05:46:21Zoai:run.unl.pt:10362/163239Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T03:59:19.295294Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
Compressed AFM-IR hyperspectral nanoimaging |
title |
Compressed AFM-IR hyperspectral nanoimaging |
spellingShingle |
Compressed AFM-IR hyperspectral nanoimaging Kästner, B. AFM-IR hyperspectral nanoimaging Leishmania parasites low-rank matrix reconstruction Instrumentation Engineering (miscellaneous) Applied Mathematics SDG 3 - Good Health and Well-being SDG 9 - Industry, Innovation, and Infrastructure |
title_short |
Compressed AFM-IR hyperspectral nanoimaging |
title_full |
Compressed AFM-IR hyperspectral nanoimaging |
title_fullStr |
Compressed AFM-IR hyperspectral nanoimaging |
title_full_unstemmed |
Compressed AFM-IR hyperspectral nanoimaging |
title_sort |
Compressed AFM-IR hyperspectral nanoimaging |
author |
Kästner, B. |
author_facet |
Kästner, B. Marschall, M. Hornemann, A. Metzner, S. Patoka, P. Cortes, S. Wübbeler, G. Hoehl, A. Rühl, E. Elster, C. |
author_role |
author |
author2 |
Marschall, M. Hornemann, A. Metzner, S. Patoka, P. Cortes, S. Wübbeler, G. Hoehl, A. Rühl, E. Elster, C. |
author2_role |
author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Vector borne diseases and pathogens (VBD) Global Health and Tropical Medicine (GHTM) Instituto de Higiene e Medicina Tropical (IHMT) RUN |
dc.contributor.author.fl_str_mv |
Kästner, B. Marschall, M. Hornemann, A. Metzner, S. Patoka, P. Cortes, S. Wübbeler, G. Hoehl, A. Rühl, E. Elster, C. |
dc.subject.por.fl_str_mv |
AFM-IR hyperspectral nanoimaging Leishmania parasites low-rank matrix reconstruction Instrumentation Engineering (miscellaneous) Applied Mathematics SDG 3 - Good Health and Well-being SDG 9 - Industry, Innovation, and Infrastructure |
topic |
AFM-IR hyperspectral nanoimaging Leishmania parasites low-rank matrix reconstruction Instrumentation Engineering (miscellaneous) Applied Mathematics SDG 3 - Good Health and Well-being SDG 9 - Industry, Innovation, and Infrastructure |
description |
Funding Information: We gratefully acknowledge fruitful discussions with Alexander Govyadinov. We acknowledge financial support by Deutsche Forschungsgemeinschaft (Grants EL 492/1-1, RU 420/13-1). Sofia Cortes was supported by Fundação para a Ciência e Tecnologia (FCT) for funds to GHTM (UID/04413/2020). Publisher Copyright: © 2023 The Author(s). Published by IOP Publishing Ltd. |
publishDate |
2024 |
dc.date.none.fl_str_mv |
2024-02-08T00:17:13Z 2024-01 2024-01-01T00:00:00Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/10362/163239 |
url |
http://hdl.handle.net/10362/163239 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
0957-0233 PURE: 82852880 https://doi.org/10.1088/1361-6501/acfc27 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
8 application/pdf |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
instname_str |
Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
instacron_str |
RCAAP |
institution |
RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
collection |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository.name.fl_str_mv |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
repository.mail.fl_str_mv |
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1799138172987244544 |