{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,16]],"date-time":"2025-10-16T20:47:45Z","timestamp":1760647665262,"version":"3.38.0"},"reference-count":50,"publisher":"China Science Publishing & Media Ltd.","issue":"1","license":[{"start":{"date-parts":[[2022,8,10]],"date-time":"2022-08-10T00:00:00Z","timestamp":1660089600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["direct.mit.edu"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2023,3,8]]},"abstract":"<jats:title>ABSTRACT<\/jats:title><jats:p>In this paper, we describe the data management practices and services developed for making FAIR compliant a scientific archive of Scanning Tunneling Microscopy (STM) images. As a first step, we extracted the instrument metadata of each image of the dataset to create a structured database. We then enriched these metadata with information on the structure and composition of the surface by means of a pipeline that leverages human annotation, machine learning techniques, and instrument metadata filtering. To visually explore both images and metadata, as well as to improve the accessibility and usability of the dataset, we developed \u201cSTM explorer\u201d as a web service integrated within the Trieste Advanced Data services (TriDAS) website. On top of these data services and tools, we propose an implementation of the W3C PROV standard to describe provenance metadata of STM images.<\/jats:p>","DOI":"10.1162\/dint_a_00164","type":"journal-article","created":{"date-parts":[[2022,8,10]],"date-time":"2022-08-10T19:14:58Z","timestamp":1660158898000},"page":"27-42","update-policy":"https:\/\/doi.org\/10.1162\/mitpressjournals.corrections.policy","source":"Crossref","is-referenced-by-count":2,"title":["Towards the FAIRification of Scanning Tunneling Microscopy Images"],"prefix":"10.3724","volume":"5","author":[{"given":"Tommaso","family":"Rodani","sequence":"first","affiliation":[{"name":"AREA Science Park, Padriciano 99, 34149, Trieste, Italy"}]},{"given":"Elda","family":"Osmenaj","sequence":"additional","affiliation":[{"name":"CNR-IOM, Consiglio Nazionale delle Ricerche - Istituto Officina dei Materiali, S.S. 14 Km 163.5, Basovizza, 34149, Trieste, Italy"}]},{"given":"Alberto","family":"Cazzaniga","sequence":"additional","affiliation":[{"name":"AREA Science Park, Padriciano 99, 34149, Trieste, Italy"}]},{"given":"Mirco","family":"Panighel","sequence":"additional","affiliation":[{"name":"CNR-IOM, Consiglio Nazionale delle Ricerche - Istituto Officina dei Materiali, S.S. 14 Km 163.5, Basovizza, 34149, Trieste, Italy"}]},{"given":"Africh","family":"Cristina","sequence":"additional","affiliation":[{"name":"CNR-IOM, Consiglio Nazionale delle Ricerche - Istituto Officina dei Materiali, S.S. 14 Km 163.5, Basovizza, 34149, Trieste, Italy"}]},{"given":"Stefano","family":"Cozzini","sequence":"additional","affiliation":[{"name":"AREA Science Park, Padriciano 99, 34149, Trieste, Italy"}]}],"member":"2026","published-online":{"date-parts":[[2023,3,8]]},"reference":[{"key":"2023030801042778300_","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/sdata.2016.18","article-title":"Comment: The FAIR Guiding Principles for scientific data management and stewardship","volume":"3","author":"Wilkinson","year":"2016","journal-title":"Scientific Data"},{"volume-title":"FAIRification Process","author":"GO FAIR","key":"2023030801042778300_"},{"issue":"1-2","key":"2023030801042778300_","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1162\/dint_a_00028","article-title":"A generic workflow for the data FAIRification process","volume":"2","author":"Jacobsen","year":"2020","journal-title":"Data Intelligence"},{"issue":"S 01","key":"2023030801042778300_","doi-asserted-by":"crossref","first-page":"e21","DOI":"10.1055\/s-0040-1713684","article-title":"From raw data to FAIR data: the FAIRification workflow for health research","volume":"59","author":"Sinaci","year":"2020","journal-title":"Methods of Information in Medicine"},{"volume-title":"VT SPM Lab","author":"Scienta Omicron","key":"2023030801042778300_"},{"volume-title":"Trieste Advanced Data Services","author":"TriDAS","key":"2023030801042778300_"},{"key":"2023030801042778300_","first-page":"773","volume-title":"The W3C PROV family of specifications for modelling provenance metadata","author":"Missier","year":"2013"},{"volume-title":"Dataset of Scanning Tunneling Microscopy (STM) images of graphene on nickel","year":"2021","author":"Tommaso","key":"2023030801042778300_"},{"volume-title":"t0m-R\/STM images 0.1.0","year":"2020","author":"Tommaso","key":"2023030801042778300_"},{"key":"2023030801042778300_","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1016\/j.carbon.2020.10.019","article-title":"Strain release at the graphene-Ni(100) interface investigated by in-situ and operando scanning tunnelling microscopy","volume":"172","author":"Zou","year":"2021","journal-title":"Carbon"},{"key":"2023030801042778300_","first-page":"2105844","volume-title":"Quantum Confinement in Aligned Zigzag \u201cPseudo-Ribbons\u201d Embedded in Graphene on Ni(100)","author":"Sala","year":"2021"},{"issue":"46","key":"2023030801042778300_","doi-asserted-by":"crossref","first-page":"25308","DOI":"10.1021\/acs.jpcc.0c07251","article-title":"Honeycomb on Square Lattices: Geometric Studies and Strain Analysis of Moir'e Structures at a Symmetry-Mismatched Interface","volume":"124","author":"Zou","year":"2020","journal-title":"The Journal of Physical Chemistry C"},{"key":"2023030801042778300_","doi-asserted-by":"crossref","first-page":"528","DOI":"10.1016\/j.carbon.2020.01.039","article-title":"Operando atomic-scale study of graphene CVD growth at steps of polycrystalline nickel","volume":"161","author":"Zou","journal-title":"Carbon"},{"key":"2023030801042778300_","doi-asserted-by":"crossref","first-page":"441","DOI":"10.1016\/j.carbon.2018.01.010","article-title":"Graphene on nickel (100) micrograins: Modulating the interface interaction by extended moir'e superstructures","volume":"130","author":"Zou","year":"2018","journal-title":"Carbon"},{"issue":"21","key":"2023030801042778300_","doi-asserted-by":"crossref","first-page":"10358","DOI":"10.1039\/C9NR01072F","article-title":"Doping of epitaxial graphene by direct incorporation of nickel adatoms","volume":"11","author":"Carnevali","year":"2019","journal-title":"Nanoscale"},{"issue":"6381","key":"2023030801042778300_","doi-asserted-by":"crossref","first-page":"1243","DOI":"10.1126\/science.aan8782","article-title":"Real-time imaging of adatom-promoted graphene growth on nickel","volume":"359","author":"Patera","year":"2018","journal-title":"Science"},{"issue":"1","key":"2023030801042778300_","doi-asserted-by":"crossref","first-page":"19734","DOI":"10.1038\/srep19734","article-title":"Switchable graphene-substrate coupling through formation\/dissolution of an intercalated Ni-carbide layer","volume":"6","author":"Africh","year":"2016","journal-title":"Scientific Reports"},{"issue":"1","key":"2023030801042778300_","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1021\/nl5026985","article-title":"Temperature-Driven Changes of the Graphene Edge Structure on Ni(111): Substrate vs Hydrogen Passivation","volume":"15","author":"Patera","year":"2014","journal-title":"Nano Letters"},{"issue":"3","key":"2023030801042778300_","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1021\/jz402609d","article-title":"Atomic Scale Identification of Coexisting Graphene Structures on Ni(111)","volume":"5","author":"Bianchini","year":"2014","journal-title":"The Journal of Physical Chemistry Letters"},{"issue":"9","key":"2023030801042778300_","doi-asserted-by":"crossref","first-page":"7901","DOI":"10.1021\/nn402927q","article-title":"In Situ Observations of the Atomistic Mechanisms of Ni Catalyzed Low Temperature Graphene Growth","volume":"7","author":"Patera","year":"2013","journal-title":"ACS Nano"},{"key":"2023030801042778300_","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1016\/j.carbon.2021.01.120","article-title":"Tuning graphene doping by carbon monoxide intercalation at the Ni(111) interface","volume":"176","author":"Puppo","year":"2021","journal-title":"Carbon"},{"key":"2023030801042778300_","doi-asserted-by":"crossref","first-page":"704","DOI":"10.1016\/j.carbon.2020.09.056","article-title":"Inside out growth method for high-quality nitrogendoped graphene","volume":"171","author":"Fiori","year":"2021","journal-title":"Carbon"},{"issue":"20","key":"2023030801042778300_","doi-asserted-by":"crossref","first-page":"8887","DOI":"10.1021\/acs.jpclett.0c02447","article-title":"Mechanism of CO Intercalation through the Graphene\/Ni(111) Interface and Effect of Doping","volume":"11","author":"Perilli","year":"2020","journal-title":"The Journal of Physical Chemistry Letters"},{"issue":"8","key":"2023030801042778300_","doi-asserted-by":"crossref","first-page":"1798","DOI":"10.1109\/TPAMI.2013.50","article-title":"Representation learning: a review and new perspectives","volume":"35","author":"Bengio","year":"2013","journal-title":"IEEE transactions on pattern analysis and machine intelligence"},{"issue":"11","key":"2023030801042778300_","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1109\/35.41400","article-title":"Handwritten digit recognition: applications of neural network chips and automatic learning","volume":"27","author":"Le Cun","year":"1989","journal-title":"IEEE Communications Magazine"},{"volume-title":"Deep Learning","year":"2016","author":"Goodfellow","key":"2023030801042778300_"},{"issue":"10","key":"2023030801042778300_","doi-asserted-by":"crossref","first-page":"1345","DOI":"10.1109\/TKDE.2009.191","article-title":"A Survey on Transfer Learning","volume":"22","author":"Pan","year":"2010","journal-title":"IEEE Transactions on Knowledge and Data Engineering"},{"volume-title":"What makes ImageNet good for transfer learning? NeurIPS LSCVS 2016 Workshop","year":"2016","author":"Huh","key":"2023030801042778300_"},{"key":"2023030801042778300_","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-017-13565-z","article-title":"Neural Network for Nanoscience Scanning Electron Microscope Image Recognition","volume":"7","author":"Modarres","year":"2017","journal-title":"Scientific Reports"},{"issue":"4","key":"2023030801042778300_","doi-asserted-by":"crossref","first-page":"513","DOI":"10.1162\/dint_a_00062","article-title":"Deep Learning, Feature Learning, and Clustering Analysis for SEM Image Classification","volume":"2","author":"Aversa","year":"2020","journal-title":"Data Intelligence"},{"volume-title":"Representation Learning and Hierarchical Clustering for microscopy images","year":"2020","author":"Cazzaniga","key":"2023030801042778300_"},{"key":"2023030801042778300_","first-page":"248","volume-title":"Imagenet: A large-scale hierarchical image database","author":"Deng","year":"2009"},{"key":"2023030801042778300_","doi-asserted-by":"crossref","DOI":"10.1109\/CVPR.2016.90","volume-title":"Deep Residual Learning for Image Recognition","author":"He","year":"2016"},{"volume-title":"Machine Learning techniques and visualization tools for STM images at CNR-IOM labs","year":"2020","author":"Rodani","key":"2023030801042778300_"},{"volume-title":"Bokeh: Python library for interactive visualization","year":"2020","author":"Bokeh Development Team","key":"2023030801042778300_"},{"volume-title":"rescipy-project\/spym: v0.7.0","year":"2021","author":"Panighel","key":"2023030801042778300_"},{"volume-title":"Flask web development: developing web applications with python","year":"2018","author":"Grinberg","key":"2023030801042778300_"},{"issue":"12","key":"2023030801042778300_","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1109\/MC.2007.421","article-title":"Examining the Challenges of Scientific Workflows","volume":"40","author":"Gil","year":"2007","journal-title":"Computer"},{"key":"2023030801042778300_","first-page":"15","article-title":"Prov-dm: The prov data model","volume":"14","author":"Belhajjame","year":"2013","journal-title":"W3C Recommendation"},{"volume-title":"An Overview of the PROV Family of Documents","year":"2013","author":"PROV-Overview","key":"2023030801042778300_"},{"volume-title":"NFFA Glossary","author":"NFFA","key":"2023030801042778300_"},{"volume-title":"Integrated Model and Data Driven Materials Characterization","author":"MDMC","key":"2023030801042778300_"},{"volume-title":"PROV-O: The PROV Ontology. English. W3C Recommendation","year":"2013","author":"Lebo","key":"2023030801042778300_"},{"volume-title":"Prov Python","year":"2014","author":"Trung Dong","key":"2023030801042778300_"},{"volume-title":"F-UJI - An Automated FAIR Data Assessment Tool","year":"2020","author":"Devaraju","key":"2023030801042778300_"},{"volume-title":"Learning from labeled and unlabeled data with label propagation","year":"2002","author":"Zhu","key":"2023030801042778300_"},{"volume-title":"Machine learning: a probabilistic perspective","year":"2012","author":"Murphy","key":"2023030801042778300_"},{"key":"2023030801042778300_","first-page":"560","volume-title":"Active provenance for Data-Intensive workflows: engaging users and developers","author":"Spinuso","year":"2019"},{"volume-title":"rescipy-project\/nxstm: v0.3.0","year":"2021","author":"Panighel","key":"2023030801042778300_"},{"issue":"1","key":"2023030801042778300_","doi-asserted-by":"crossref","first-page":"181","DOI":"10.2478\/s11534-011-0096-2","article-title":"Gwyddion: an open-source software for SPM data analysis","volume":"10","author":"N\u011bcas","year":"2012","journal-title":"Open Physics"}],"container-title":["Data Intelligence"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/direct.mit.edu\/dint\/article-pdf\/5\/1\/27\/2074268\/dint_a_00164.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/direct.mit.edu\/dint\/article-pdf\/5\/1\/27\/2074268\/dint_a_00164.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,3,14]],"date-time":"2025-03-14T07:43:16Z","timestamp":1741938196000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.sciengine.com\/doi\/10.1162\/dint_a_00164"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023]]},"references-count":50,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2023,3,8]]}},"URL":"https:\/\/doi.org\/10.1162\/dint_a_00164","relation":{},"ISSN":["2641-435X"],"issn-type":[{"type":"electronic","value":"2641-435X"}],"subject":[],"published-other":{"date-parts":[[2023]]},"published":{"date-parts":[[2023]]}}}