{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,8,3]],"date-time":"2025-08-03T04:07:00Z","timestamp":1754194020915,"version":"3.37.3"},"reference-count":27,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2017,7,11]],"date-time":"2017-07-11T00:00:00Z","timestamp":1499731200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2017,7,11]],"date-time":"2017-07-11T00:00:00Z","timestamp":1499731200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Data"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Using a scanning near-field optical microscope coupled to an infrared free electron laser (SNOM-IR-FEL) in low-resolution transmission mode, we collected chemical data from whole cervical cells obtained from 5 pre-menopausal, non-pregnant women of reproductive age, and cytologically classified as normal or with different grades of cervical cell dyskaryosis. Imaging data are complemented by demography. All samples were collected before any treatment. Spectra were also collected using attenuated total reflection, Fourier-transform (ATR-FTIR) spectroscopy, to investigate the differences between the two techniques. Results of this pilot study suggests SNOM-IR-FEL may be able to distinguish cervical abnormalities based upon changes in the chemical profiles for each grade of dyskaryosis at designated wavelengths associated with DNA, Amide I\/II, and lipids. The novel data sets are the first collected using SNOM-IR-FEL in transmission mode at the ALICE facility (UK), and obtained using whole cells as opposed to tissue sections, thus providing an \u2018intact\u2019 chemical profile. These data sets are suited to complementing future work on image analysis, and\/or applying the newly developed algorithm to other datasets collected using the SNOM-IR-FEL approach.<\/jats:p>","DOI":"10.1038\/sdata.2017.84","type":"journal-article","created":{"date-parts":[[2017,7,11]],"date-time":"2017-07-11T13:31:06Z","timestamp":1499779866000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["An imaging dataset of cervical cells using scanning near-field optical microscopy coupled to an infrared free electron laser"],"prefix":"10.1038","volume":"4","author":[{"given":"Diane E.","family":"Halliwell","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Camilo L.M.","family":"Morais","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"K\u00e1ssio M.G.","family":"Lima","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J\u00falio","family":"Trevisan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michele R.F.","family":"Siggel-King","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tim","family":"Craig","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"James","family":"Ingham","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David S.","family":"Martin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kelly","family":"Heys","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maria","family":"Kyrgiou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0236-795X","authenticated-orcid":false,"given":"Anita","family":"Mitra","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Evangelos","family":"Paraskevaidis","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Georgios","family":"Theophilou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pierre L.","family":"Martin-Hirsch","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8581-3478","authenticated-orcid":false,"given":"Antonio","family":"Cricenti","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marco","family":"Luce","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter","family":"Weightman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8562-4944","authenticated-orcid":false,"given":"Francis L.","family":"Martin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2017,7,11]]},"reference":[{"key":"BFsdata201784_CR1","doi-asserted-by":"publisher","first-page":"11449","DOI":"10.1021\/ac4025889","volume":"85","author":"AJ Harrison","year":"2013","unstructured":"Harrison, A. J., Bilgili, E. A., Beaudoin, S. P. & Taylor, L. S. Atomic force microscope infrared spectroscopy of griseofulvin nanocrystals. Anal. Chem. 85, 11449\u201311455 (2013).","journal-title":"Anal. Chem."},{"key":"BFsdata201784_CR2","doi-asserted-by":"publisher","first-page":"e31592","DOI":"10.1371\/journal.pone.0031592","volume":"7","author":"K-AD Walker","year":"2012","unstructured":"Walker, K-A. D., Morgan, C., Doak, S. H. & Dunstan, P. R. Quantum dots for multiplexed detection and characterisation of prostate cancer cells using a scanning near-field optical microscope. PLoS ONE 7, e31592 (2012).","journal-title":"PLoS ONE"},{"key":"BFsdata201784_CR3","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12951-014-0061-5","volume":"13","author":"L Andolfi","year":"2015","unstructured":"Andolfi, L. et al. The application of scanning near field optical imaging to the study of human sperm morphology. J Nanobiotechnology 13, 1\u201311 (2015).","journal-title":"J Nanobiotechnology"},{"key":"BFsdata201784_CR4","doi-asserted-by":"publisher","first-page":"642","DOI":"10.1016\/j.colsurfa.2007.04.173","volume":"313\u2013314","author":"L Zhong","year":"2008","unstructured":"Zhong, L., Liao, W., Wang, X. & Cai, J. Detection the specific marker of CD3 molecules of human peripheral T lymphocytes using SNOM and quantum dots. Colloids and Surfaces A: Physiochem. Eng. Aspects 313\u2013314, 642\u2013646 (2008).","journal-title":"Colloids and Surfaces A: Physiochem. Eng. Aspects"},{"key":"BFsdata201784_CR5","doi-asserted-by":"publisher","first-page":"053701","DOI":"10.1063\/1.4790436","volume":"102","author":"AD Smith","year":"2013","unstructured":"Smith, A. D. et al. Near-field optical microscopy with an infra-red free electron laser applied to cancer diagnosis. Appl. Phys. Lett. 102, 053701 (2013).","journal-title":"Appl. Phys. Lett."},{"key":"BFsdata201784_CR6","doi-asserted-by":"publisher","first-page":"2738","DOI":"10.1039\/b109279k","volume":"4","author":"A Cricenti","year":"2002","unstructured":"Cricenti, A. et al. Very high resolution near-field chemical imaging using an infrared free electron laser. Phys. Chem. Chem. Phys. 4, 2738\u20132741 (2002).","journal-title":"Phys. Chem. Chem. Phys."},{"key":"BFsdata201784_CR7","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1016\/j.nima.2012.02.049","volume":"680","author":"NR Thompson","year":"2012","unstructured":"Thompson, N. R. et al. First lasing of the ALICE infra-red free-electron laser. Nucl. Instrum. Methods Phys. Res. A 680, 117\u2013123 (2012).","journal-title":"Nucl. Instrum. Methods Phys. Res. A"},{"unstructured":"Saveliev, Y. et al. Recent developments on ALICE (Accelerators and Lasers in Combined Experiments) at Daresbury laboratory IPAC\u201910, Kyoto, Japan, 2010: (TUPE096).","key":"BFsdata201784_CR8"},{"unstructured":"Thompson, N. R. et al. Status of the ALICE IR-FEL: from ERL demonstrator to user facility. International Free Electron Laser Conference\u2014FEL 2015, Daejon, Korea, 2014: (TUP015).","key":"BFsdata201784_CR9"},{"key":"BFsdata201784_CR10","doi-asserted-by":"publisher","first-page":"1353","DOI":"10.1242\/dmm.011338","volume":"6","author":"F Baenke","year":"2013","unstructured":"Baenke, F., Peck, B., Miess, H. & Schulze, A. Hooked on fat: the role of lipid synthesis in cancer metabolism and tumour development. Dis. Model Mech. 6, 1353\u20131363 (2013).","journal-title":"Dis. Model Mech."},{"key":"BFsdata201784_CR11","doi-asserted-by":"publisher","first-page":"134","DOI":"10.1080\/05704920701829043","volume":"43","author":"Z Movasaghi","year":"2008","unstructured":"Movasaghi, Z., Rehman, S. & ur Rehman, I. Fourier transform infrared (FTIR) spectroscopy of biological materials. Appl. Spectrosc. Rev. 43, 134\u2013179 (2008).","journal-title":"Appl. Spectrosc. Rev."},{"key":"BFsdata201784_CR12","doi-asserted-by":"publisher","first-page":"4576","DOI":"10.1039\/C3AY42224K","volume":"6","author":"NC Purandare","year":"2014","unstructured":"Purandare, N. C. et al. Infrared spectroscopy with multivariate analysis segregates low-grade cervical cytology based on likelihood to regress, remain static or progress. Anal. Methods 6, 4576\u20134584 (2014).","journal-title":"Anal. Methods"},{"key":"BFsdata201784_CR13","doi-asserted-by":"publisher","first-page":"3909","DOI":"10.1039\/c3an36527a","volume":"138","author":"NC Purandare","year":"2013","unstructured":"Purandare, N. C. et al. Biospectroscopy insights into the multi-stage process of cervical cancer development: probing for spectral biomarkers in cytology to distinguish grades. Analyst 138, 3909\u20133916 (2013).","journal-title":"Analyst"},{"key":"BFsdata201784_CR14","doi-asserted-by":"publisher","first-page":"29494","DOI":"10.1038\/srep29494","volume":"6","author":"DE Halliwell","year":"2016","unstructured":"Halliwell, D. E. et al. Imaging cervical cytology with scanning near-field optical microscopy (SNOM) coupled with an IR-FEL. Sci. Rep. 6, 29494 (2016).","journal-title":"Sci. Rep."},{"key":"BFsdata201784_CR15","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1155\/2005\/798710","volume":"16","author":"F Coutl\u00e9e","year":"2005","unstructured":"Coutl\u00e9e, F., Rouleau, D., Ferenczy, A. & Franco, E. The laboratory diagnosis of genital human papillomavirus infections. Can. J. Infect. Dis. Med. Microbiol. 16, 83\u201391 (2005).","journal-title":"Can. J. Infect. Dis. Med. Microbiol."},{"key":"BFsdata201784_CR16","volume-title":"Achievable standards, benchmarks for reporting, and criteria for evaluating cervical cytopathology","author":"JHF Smith","year":"2013","unstructured":"NHSCSP. Achievable standards, benchmarks for reporting, and criteria for evaluating cervical cytopathology 3rd edn (eds Smith, J. H. F., Patnic, J. & Chapman, K. ) (NHS Cancer Screening Programme, 2013)."},{"key":"BFsdata201784_CR17","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1159\/000381842","volume":"59","author":"R Nayar","year":"2015","unstructured":"Nayar, R. & Wilbur, D. C. The Pap Test and Bethesda 2014. Acta Cytologica 59, 121\u2013132 (2015).","journal-title":"Acta Cytologica"},{"doi-asserted-by":"publisher","unstructured":"Halliwell, D. E. Biospectroscopy Investigations into Cervical Cytology, (MSc by Research Dissertation, Lancaster University, LEC, June 2016, doi:10.13140\/RG.2.2.34170.90561).","key":"BFsdata201784_CR18","DOI":"10.13140\/RG.2.2.34170.90561"},{"key":"BFsdata201784_CR19","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.canlet.2006.03.019","volume":"246","author":"MJ Walsh","year":"2007","unstructured":"Walsh, M. J. et al. IR microspectroscopy: potential applications in cervical cancer screening. Cancer Lett. 246, 1\u201311 (2007).","journal-title":"Cancer Lett."},{"unstructured":"Uphoff, T. The Evolving Role of HPV Testing in Cervical Cancer Screening. American Association for Clinical Chemistry (AACC).https:\/\/www.aacc.org\/publications\/cln\/articles\/2014\/april\/cervical-cancer.","key":"BFsdata201784_CR20"},{"key":"BFsdata201784_CR21","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1186\/1471-2407-11-263","volume":"11","author":"E Cocco","year":"2011","unstructured":"Cocco, E. et al. Expression of Tissue factor in Adenocarcinoma and Squamous Cell Carcinoma of the Uterine Cervix: Implications for immunotherapy with hI-con1, a factor VII-IgGFc chimeric protein targeting tissue factor. BMC Cancer 11, 263 (2011).","journal-title":"BMC Cancer"},{"key":"BFsdata201784_CR22","doi-asserted-by":"publisher","first-page":"261","DOI":"10.1038\/modpathol.3880047","volume":"13","author":"RJ Zaino","year":"2000","unstructured":"Zaino, R. J. The 1999 Long Course on Pathology of the Uterine Corpus and Cervix: Glandular Lesions of the Uterine Cervix. Mod Pathol. 13, 261\u2013274 (2000).","journal-title":"Mod Pathol."},{"key":"BFsdata201784_CR23","doi-asserted-by":"publisher","first-page":"585","DOI":"10.1039\/C5AN00939A","volume":"141","author":"G Theophilou","year":"2016","unstructured":"Theophilou, G. et al. ATR-FTIR spectroscopy coupled with chemometric analysis discriminates normal, borderline and malignant ovarian tissue: classifying subtypes of human cancer. Analyst 141, 585\u2013594 (2016).","journal-title":"Analyst"},{"key":"BFsdata201784_CR24","doi-asserted-by":"publisher","first-page":"1580","DOI":"10.1590\/S0103-50532007000800021","volume":"18","author":"RKH Galv\u00e3o","year":"2007","unstructured":"Galv\u00e3o, R. K. H., Ara\u00fajo, M. C. U., Silva, E. C., Jos\u00e9, G. E., Soares, S. F. C. & Paiva, H. M. Cross-validation for the selection of spectral variables using the successive projections algorithm. J. Braz. Chem. Soc 18, 1580\u20131584 (2007).","journal-title":"J. Braz. Chem. Soc"},{"key":"BFsdata201784_CR25","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1080\/00401706.1969.10490666","volume":"11","author":"RW Kennard","year":"1969","unstructured":"Kennard, R. W. & Stone, L. A. Computer aided design of experiments. Technometrics 11, 137\u2013148 (1969).","journal-title":"Technometrics"},{"key":"BFsdata201784_CR26","doi-asserted-by":"publisher","first-page":"1095","DOI":"10.1093\/bioinformatics\/btt084","volume":"29","author":"J Trevisan","year":"2013","unstructured":"Trevisan, J., Angelov, P. P., Scott, A. D., Carmichael, P. L. & Martin, F. L. IRootLab: a free and open-source MATLAB toolbox for vibrational biospectroscopy data analysis. Bioinformatics 29, 1095\u20131097 (2013).","journal-title":"Bioinformatics"},{"key":"BFsdata201784_CR27","doi-asserted-by":"publisher","DOI":"10.6084\/m9.figshare.3971883","author":"D. E. Halliwell","year":"2016","unstructured":"Halliwell, D. E., Morais, C. L. M., & Lima, K. M. G. Figshare https:\/\/doi.org\/10.6084\/m9.figshare.3971883 (2016)"}],"container-title":["Scientific Data"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/sdata201784.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/sdata201784","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/sdata201784","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"},{"URL":"https:\/\/www.nature.com\/articles\/sdata201784.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,12,23]],"date-time":"2022-12-23T03:07:26Z","timestamp":1671764846000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/sdata201784"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,7,11]]},"references-count":27,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2017,12,19]]}},"alternative-id":["BFsdata201784"],"URL":"https:\/\/doi.org\/10.1038\/sdata.2017.84","relation":{"references":[{"id-type":"doi","id":"10.6084\/m9.figshare.3971883","asserted-by":"subject"}]},"ISSN":["2052-4463"],"issn-type":[{"type":"electronic","value":"2052-4463"}],"subject":[],"published":{"date-parts":[[2017,7,11]]},"assertion":[{"value":"30 September 2016","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 May 2017","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"11 July 2017","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing financial interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"170084"}}