{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,17]],"date-time":"2025-10-17T00:18:15Z","timestamp":1760660295242,"version":"build-2065373602"},"reference-count":28,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2025,9,19]],"date-time":"2025-09-19T00:00:00Z","timestamp":1758240000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004727","name":"Flanders Institute for Biotechnology","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004727","id-type":"DOI","asserted-by":"publisher"}]},{"name":"University of Leuven","award":["I011220N","1128822N"],"award-info":[{"award-number":["I011220N","1128822N"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,10,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Atomic Force Microscopy-based Infrared spectroscopy (AFM-IR) is a novel and innovative method for label-free high-resolution structural biology. However, the nature of the data files generated by AFM-IR instruments precludes investigation by conventional open-source scientific image analysis software suites. As a result, reporting of AFM-IR datasets is not standardized and the data itself is difficult to audit.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We have developed a web application that allows anyone to open, review, and audit raw AFM-IR data files easily and without deep knowledge of the method. It also exposes all metadata recorded by the microscope at the time of measurement. The web application is based on a Python package that supports custom data analyses within the scientific Python ecosystem. This tool provides an accessible, transparent solution for AFM-IR data review, with the potential to support reproducibility and standardization in AFM-IR research and encourage wider adoption of this innovative spectroscopy method.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The web app is hosted at https:\/\/anasys-python-tools-gui.streamlit.app. Its source code is listed at https:\/\/github.com\/wduverger\/anasys-python-tools-gui. The underlying Python package is available at https:\/\/github.com\/GeorgRamer\/anasys-python-tools and can be installed using pip.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf513","type":"journal-article","created":{"date-parts":[[2025,9,20]],"date-time":"2025-09-20T02:46:35Z","timestamp":1758336395000},"source":"Crossref","is-referenced-by-count":0,"title":["AXZ viewer: a web application to visualize unprocessed AFM-IR data"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6851-7247","authenticated-orcid":false,"given":"Wouter","family":"Duverger","sequence":"first","affiliation":[{"name":"Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research , Leuven 3000,","place":["Belgium"]},{"name":"Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven , Leuven 3000,","place":["Belgium"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8307-5435","authenticated-orcid":false,"given":"Georg","family":"Ramer","sequence":"additional","affiliation":[{"name":"Institute of Chemical Technologies and Analytics, TU Wien , Vienna 1060,","place":["Austria"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4030-1022","authenticated-orcid":false,"given":"Nikolaos","family":"Louros","sequence":"additional","affiliation":[{"name":"Center for Alzheimer\u2019s and Neurodegenerative Diseases, Peter O\u2019Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center , Dallas, TX 75390,","place":["United States"]},{"name":"Department of Biophysics, University of Texas Southwestern Medical Center , Dallas, TX 75390,","place":["United States"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2020-0168","authenticated-orcid":false,"given":"Joost","family":"Schymkowitz","sequence":"additional","affiliation":[{"name":"Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research , Leuven 3000,","place":["Belgium"]},{"name":"Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven , Leuven 3000,","place":["Belgium"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9189-7399","authenticated-orcid":false,"given":"Frederic","family":"Rousseau","sequence":"additional","affiliation":[{"name":"Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research , Leuven 3000,","place":["Belgium"]},{"name":"Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven , Leuven 3000,","place":["Belgium"]}]}],"member":"286","published-online":{"date-parts":[[2025,9,19]]},"reference":[{"key":"2025101607402885300_btaf513-B1","doi-asserted-by":"publisher","first-page":"150","DOI":"10.1016\/j.aca.2020.04.015","article-title":"Biomolecular and bioanalytical applications of infrared spectroscopy\u2014a review","volume":"1133","author":"Bec","year":"2020","journal-title":"Anal Chim Acta"},{"key":"2025101607402885300_btaf513-B2","doi-asserted-by":"publisher","first-page":"6676","DOI":"10.1021\/acssuschemeng.3c00199","article-title":"Sustainable immiscible polylactic acid (PLA) and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) blends: crystallization and foaming behavior","volume":"11","author":"Br\u00fctting","year":"2023","journal-title":"ACS Sustain Chem Eng"},{"key":"2025101607402885300_btaf513-B3","doi-asserted-by":"publisher","first-page":"163","DOI":"10.1111\/jmi.13193","article-title":"Towards artefact-free AFM image presentation and interpretation","volume":"291","author":"Burnham","year":"2023","journal-title":"J Microsc"},{"key":"2025101607402885300_btaf513-B4","doi-asserted-by":"publisher","first-page":"A2","DOI":"10.1051\/0004-6361\/202244702","article-title":"Chemical composition of carbonaceous asteroid Ryugu from synchrotron spectroscopy in the mid- to far-infrared of Hayabusa2-returned samples","volume":"671","author":"Dartois","year":"2023","journal-title":"Astronomy Astrophysics"},{"key":"2025101607402885300_btaf513-B5","doi-asserted-by":"publisher","first-page":"124519","DOI":"10.1063\/1.3429214","article-title":"Theory of infrared nanospectroscopy by photothermal induced resonance","volume":"107","author":"Dazzi","year":"2010","journal-title":"J Appl Phys"},{"key":"2025101607402885300_btaf513-B6","doi-asserted-by":"publisher","first-page":"5146","DOI":"10.1021\/acs.chemrev.6b00448","article-title":"AFM-IR: technology and applications in nanoscale infrared spectroscopy and chemical imaging","volume":"117","author":"Dazzi","year":"2017","journal-title":"Chem Rev"},{"key":"2025101607402885300_btaf513-B7","doi-asserted-by":"publisher","first-page":"1538","DOI":"10.1177\/00037028211050659","article-title":"Revealing lipid body formation and its subcellular reorganization in oleaginous microalgae using correlative optical microscopy and infrared nanospectroscopy","volume":"75","author":"Deniset-Besseau","year":"2021","journal-title":"Appl Spectrosc"},{"key":"2025101607402885300_btaf513-B8","doi-asserted-by":"publisher","first-page":"15719","DOI":"10.1021\/acs.analchem.0c02228","article-title":"Nanoscale infrared spectroscopy and chemometrics enable detection of intracellular protein distribution","volume":"92","author":"Dos Santos","year":"2020","journal-title":"Anal Chem"},{"key":"2025101607402885300_btaf513-B9","doi-asserted-by":"publisher","first-page":"301","DOI":"10.1021\/acsmeasuresciau.3c00010","article-title":"AFM-IR for nanoscale chemical characterization in life sciences: recent developments and future directions","volume":"3","author":"Dos Santos","year":"2023","journal-title":"ACS Meas Sci Au"},{"key":"2025101607402885300_btaf513-B10","doi-asserted-by":"publisher","first-page":"406","DOI":"10.1186\/s12951-024-02674-3","article-title":"An end-to-end approach for single-cell infrared absorption spectroscopy of bacterial inclusion bodies: from AFM-IR measurement to data interpretation of large sample sets","volume":"22","author":"Duverger","year":"2024","journal-title":"J Nanobiotechnol"},{"key":"2025101607402885300_btaf513-B11","doi-asserted-by":"publisher","first-page":"10","DOI":"10.5334\/jors.148","article-title":"xarray: N-D labeled arrays and datasets in Python","volume":"5","author":"Hoyer","year":"2017","journal-title":"J Open Res Softw"},{"key":"2025101607402885300_btaf513-B12","doi-asserted-by":"publisher","first-page":"e108","DOI":"10.1093\/nar\/gkz630","article-title":"Infrared nanospectroscopic mapping of a single metaphase chromosome","volume":"47","author":"Lipiec","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2025101607402885300_btaf513-B13","doi-asserted-by":"publisher","first-page":"2909","DOI":"10.1039\/D0TB02584D","article-title":"AFM-IR probing the influence of polarization on the expression of proteins within single macrophages","volume":"9","author":"Liu","year":"2021","journal-title":"J Mater Chem B"},{"key":"2025101607402885300_btaf513-B14","doi-asserted-by":"publisher","first-page":"P3018","DOI":"10.1149\/2.0041604jss","article-title":"Nanoscale chemical-mechanical characterization of nanoelectronic low-kDielectric\/Cu interconnects","volume":"5","author":"Lo","year":"2016","journal-title":"ECS J Solid State Sci Technol"},{"key":"2025101607402885300_btaf513-B15","doi-asserted-by":"publisher","first-page":"181","DOI":"10.2478\/s11534-011-0096-2","article-title":"Gwyddion: an open-source software for SPM data analysis","volume":"10","author":"Ne\u010das","year":"2012","journal-title":"Open Phys"},{"key":"2025101607402885300_btaf513-B16","doi-asserted-by":"publisher","first-page":"1700457","DOI":"10.1002\/ppsc.201700457","article-title":"High-resolution label-free detection of biocompatible polymeric nanoparticles in cells","volume":"35","author":"Pancani","year":"2018","journal-title":"Particle Particle Syst Characterization"},{"key":"2025101607402885300_btaf513-B17","doi-asserted-by":"publisher","first-page":"3140","DOI":"10.1021\/acs.analchem.7b04318","article-title":"Multispectral atomic force microscopy-infrared nano-imaging of malaria infected red blood cells","volume":"90","author":"Perez-Guaita","year":"2018","journal-title":"Anal Chem"},{"key":"2025101607402885300_btaf513-B18","doi-asserted-by":"publisher","first-page":"553","DOI":"10.5802\/crchim.210","article-title":"Multiscale approach to provide a better physicochemical description of women breast microcalcifications","volume":"25","author":"Petay","year":"2022","journal-title":"Comptes Rendus Chimie"},{"key":"2025101607402885300_btaf513-B19","doi-asserted-by":"publisher","first-page":"2977","DOI":"10.1007\/s00216-012-5765-5","article-title":"FTIR imaging investigation in MIR and in an enlarged MIR-NIR spectral range","volume":"402","author":"Poli","year":"2012","journal-title":"Anal Bioanal Chem"},{"key":"2025101607402885300_btaf513-B20","doi-asserted-by":"publisher","first-page":"3544","DOI":"10.1021\/acs.analchem.9b03468","article-title":"Understanding and controlling spatial resolution, sensitivity, and surface selectivity in resonant-mode photothermal-induced resonance spectroscopy","volume":"92","author":"Quaroni","year":"2020","journal-title":"Anal Chem"},{"key":"2025101607402885300_btaf513-B21","doi-asserted-by":"publisher","first-page":"13524","DOI":"10.1021\/acs.analchem.7b03878","article-title":"Quantitative chemical analysis at the nanoscale using the photothermal induced resonance technique","volume":"89","author":"Ramer","year":"2017","journal-title":"Anal Chem"},{"key":"2025101607402885300_btaf513-B22","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1117\/12.2651424","article-title":"Image processing as basis for chemometrics in photothermal atomic force microscopy infrared imaging","volume":"12392","author":"Ramer","year":"2023","journal-title":"Adv Chem Microscopy Life Sci Transl Med"},{"key":"2025101607402885300_btaf513-B23","doi-asserted-by":"publisher","first-page":"425502","DOI":"10.1088\/1361-6528\/ab31dd","article-title":"Nanoscale AFM-IR spectroscopic imaging of lipid heterogeneity and effect of irradiation in prostate cancer cells","volume":"30","author":"Roman","year":"2019","journal-title":"Nanotechnology"},{"key":"2025101607402885300_btaf513-B24","doi-asserted-by":"publisher","first-page":"134","DOI":"10.1016\/j.abb.2019.02.001","article-title":"Atomic force microscopy for single molecule characterisation of protein aggregation","volume":"664","author":"Ruggeri","year":"2019","journal-title":"Arch Biochem Biophys"},{"key":"2025101607402885300_btaf513-B25","doi-asserted-by":"publisher","first-page":"2300","DOI":"10.3390\/cells10092300","article-title":"Quasar: easy machine learning for biospectroscopy","volume":"10","author":"Toplak","year":"2021","journal-title":"Cells"},{"key":"2025101607402885300_btaf513-B26","doi-asserted-by":"publisher","first-page":"8536","DOI":"10.1021\/acsapm.2c01453","article-title":"Photoinduced alignment under solvent vapor annealing (PA-SVA): enhanced ordering and patterning in block copolymer films","volume":"4","author":"Tseng","year":"2022","journal-title":"ACS Appl Polym Mater"},{"key":"2025101607402885300_btaf513-B27","doi-asserted-by":"publisher","first-page":"132","DOI":"10.1039\/d0an01545h","article-title":"Probing amyloid fibril secondary structures by infrared nanospectroscopy: experimental and theoretical considerations","volume":"146","author":"Waeytens","year":"2021","journal-title":"Analyst"},{"key":"2025101607402885300_btaf513-B28","doi-asserted-by":"publisher","first-page":"1500615","DOI":"10.1002\/aenm.201500615","article-title":"Photovoltaic switching mechanism in lateral structure hybrid perovskite solar cells","volume":"5","author":"Yuan","year":"2015","journal-title":"Adv Energy Mater"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaf513\/64326169\/btaf513.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/10\/btaf513\/64326169\/btaf513.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/10\/btaf513\/64326169\/btaf513.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,16]],"date-time":"2025-10-16T11:40:33Z","timestamp":1760614833000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btaf513\/8258674"}},"subtitle":[],"editor":[{"given":"Xin","family":"Gao","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2025,9,19]]},"references-count":28,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2025,10,2]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaf513","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2025,10]]},"published":{"date-parts":[[2025,9,19]]},"article-number":"btaf513"}}