{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T11:50:36Z","timestamp":1788954636680,"version":"build-2803163510"},"reference-count":50,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2021,12,10]],"date-time":"2021-12-10T00:00:00Z","timestamp":1639094400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003627","name":"Rural Development Administration","doi-asserted-by":"publisher","award":["PJ01416803"],"award-info":[{"award-number":["PJ01416803"]}],"id":[{"id":"10.13039\/501100003627","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Plants"],"abstract":"<jats:p>Stomatal observation and automatic stomatal detection are useful analyses of stomata for taxonomic, biological, physiological, and eco-physiological studies. We present a new clearing method for improved microscopic imaging of stomata in soybean followed by automated stomatal detection by deep learning. We tested eight clearing agent formulations based upon different ethanol and sodium hypochlorite (NaOCl) concentrations in order to improve the transparency in leaves. An optimal formulation\u2014a 1:1 (v\/v) mixture of 95% ethanol and NaOCl (6\u201314%)\u2014produced better quality images of soybean stomata. Additionally, we evaluated fixatives and dehydrating agents and selected absolute ethanol for both fixation and dehydration. This is a good substitute for formaldehyde, which is more toxic to handle. Using imaging data from this clearing method, we developed an automatic stomatal detector using deep learning and improved a deep-learning algorithm that automatically analyzes stomata through an object detection model using YOLO. The YOLO deep-learning model successfully recognized stomata with high mAP (~0.99). A web-based interface is provided to apply the model of stomatal detection for any soybean data that makes use of the new clearing protocol.<\/jats:p>","DOI":"10.3390\/plants10122714","type":"journal-article","created":{"date-parts":[[2021,12,10]],"date-time":"2021-12-10T08:17:58Z","timestamp":1639124278000},"page":"2714","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["Optimizing the Experimental Method for Stomata-Profiling Automation of Soybean Leaves Based on Deep Learning"],"prefix":"10.3390","volume":"10","author":[{"given":"Syada Nizer","family":"Sultana","sequence":"first","affiliation":[{"name":"Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Halim","family":"Park","sequence":"additional","affiliation":[{"name":"Division of Bio & Medical Big Data Department (BK4 Program), Gyeongsang National University, Jinju 52828, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sung Hoon","family":"Choi","sequence":"additional","affiliation":[{"name":"Division of Bio & Medical Big Data Department (BK4 Program), Gyeongsang National University, Jinju 52828, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2741-4049","authenticated-orcid":false,"given":"Hyun","family":"Jo","sequence":"additional","affiliation":[{"name":"Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2052-6582","authenticated-orcid":false,"given":"Jong Tae","family":"Song","sequence":"additional","affiliation":[{"name":"Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3474-0384","authenticated-orcid":false,"given":"Jeong-Dong","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea"},{"name":"Department of Integrative Biology, Kyungpook National University, Daegu 41566, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4313-7088","authenticated-orcid":false,"given":"Yang Jae","family":"Kang","sequence":"additional","affiliation":[{"name":"Division of Bio & Medical Big Data Department (BK4 Program), Gyeongsang National University, Jinju 52828, Korea"},{"name":"Division of Life Science Department, Gyeongsang National University, Jinju 52828, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,12,10]]},"reference":[{"key":"ref_1","unstructured":"Chapman, A.D. 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