{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T20:50:08Z","timestamp":1792788608929,"version":"4.5.0"},"reference-count":21,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2024,2,29]],"date-time":"2024-02-29T00:00:00Z","timestamp":1709164800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Kawasaki City","award":["Kawasaki City New Technology\/New Product Development Support Project Subsidy; Grant No. 84"],"award-info":[{"award-number":["Kawasaki City New Technology\/New Product Development Support Project Subsidy; Grant No. 84"]}]},{"name":"Kawasaki City","award":["Kawasaki City \u201cNew Normal\u201d Research and Development Subsidy; Grant No. 225"],"award-info":[{"award-number":["Kawasaki City \u201cNew Normal\u201d Research and Development Subsidy; Grant No. 225"]}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>The evaluation of the structural integrity of mechanically dynamic organs such as lungs is critical for the diagnosis of numerous pathologies and the development of therapies. This task is classically performed by histology experts in a qualitative or semi-quantitative manner. Automatic digital image processing methods appeared in the last decades, and although immensely powerful, tools are highly specialized and lack the versatility required in various experimental designs. Here, a set of scripts for the image processing software ImageJ\/Fiji to easily quantify fibrosis extend and alveolar airspace availability in Sirius Red or Masson\u2019s trichrome stained samples is presented. The toolbox consists in thirteen modules: sample detection, particles filtration (automatic and manual), border definition, air ducts identification, air ducts walls definition, parenchyma extraction, MT-staining specific pre-processing, fibrosis detection, fibrosis particles filtration, airspace detection, and visualizations (tissue only or tissue and airspace). While the process is largely automated, critical parameters are accessible to the user for increased adaptability. The modularity of the protocol allows for its adjustment to alternative experimental settings. Fibrosis and airspace can be combined as an evaluation of the structural integrity of the organ. All settings and intermediate states are saved to ensure reproducibility. These new analysis scripts allow for a rapid quantification of fibrosis and airspace in a large variety of experimental settings.<\/jats:p>","DOI":"10.1371\/journal.pone.0298015","type":"journal-article","created":{"date-parts":[[2024,2,29]],"date-time":"2024-02-29T13:30:27Z","timestamp":1709213427000},"page":"e0298015","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":15,"title":["Quantification of fibrosis extend and airspace availability in lung: A semi-automatic ImageJ\/Fiji toolbox"],"prefix":"10.1371","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8972-9786","authenticated-orcid":true,"given":"Bertrand-David","family":"S\u00e9gard","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kodai","family":"Kimura","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuimi","family":"Matsuoka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tomomi","family":"Imamura","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ayana","family":"Ikeda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Takahiro","family":"Iwamiya","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2024,2,29]]},"reference":[{"key":"pone.0298015.ref001","doi-asserted-by":"crossref","first-page":"1345","DOI":"10.1016\/S0140-6736(17)32366-8","article-title":"Global, regional, and national comparative risk assessment of 84 behavioural, environmental and occupational, and metabolic risks or clusters of risks, 1990\u20132016: a systematic analysis for the Global Burden of Disease Study 2016","volume":"390","author":"GBD 2016 Risk Factors Collaborators","year":"2017","journal-title":"Lancet"},{"key":"pone.0298015.ref002","doi-asserted-by":"crossref","first-page":"1260","DOI":"10.1016\/S0140-6736(17)32130-X","article-title":"Global, regional, and national disability-adjusted life-years (DALYs) for 333 diseases and injuries and healthy life expectancy (HALE) for 195 countries and territories, 1990\u20132016: a systematic analysis for the Global Burden of Disease Study 2016","volume":"390","author":"GBD 2016 DALYs and HALE Collaborators","year":"2017","journal-title":"Lancet"},{"key":"pone.0298015.ref003","doi-asserted-by":"crossref","first-page":"1151","DOI":"10.1016\/S0140-6736(17)32152-9","article-title":"Global, regional, and national age-sex specific mortality for 264 causes of death, 1980\u20132016: a systematic analysis for the Global Burden of Disease Study 2016","volume":"390","author":"GBD 2016 Causes of Death Collaborators","year":"2017","journal-title":"Lancet"},{"key":"pone.0298015.ref004","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1016\/j.ccm.2021.03.001","article-title":"Interstitial Lung Disease in 2020: A History of Progress","volume":"42","author":"SA Guler","year":"2021","journal-title":"Clin Chest Med"},{"key":"pone.0298015.ref005","doi-asserted-by":"crossref","first-page":"607720","DOI":"10.3389\/fmed.2021.607720","article-title":"Automated Digital Quantification of Pulmonary Fibrosis in Human Histopathology Specimens","volume":"8","author":"LC Testa","year":"2021","journal-title":"Front Med (Lausanne)"},{"key":"pone.0298015.ref006","doi-asserted-by":"crossref","first-page":"330","DOI":"10.1016\/j.ijtb.2020.11.003","article-title":"Post covid 19 pulmonary fibrosis. 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