{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,30]],"date-time":"2026-10-30T00:29:12Z","timestamp":1793320152861,"version":"4.5.0"},"reference-count":58,"publisher":"Oxford University Press (OUP)","issue":"2","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-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["INV-002830"],"award-info":[{"award-number":["INV-002830"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000199","name":"USDA","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000199","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005825","name":"NIFA","doi-asserted-by":"publisher","award":["7003146"],"award-info":[{"award-number":["7003146"]}],"id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Stomatal conductance (gs) is indicative of plant carbon dioxide uptake via photosynthesis and water loss via transpiration, making it a crucial plant biophysical trait. Direct measurement of gs is labor-intensive and usually not scalable to large fields. Using manual measurements to estimate parameters of gs models is even more labor-intensive and prone to sampling errors. This study aimed to develop an automated pipeline for gs measurement and model calibration using thermal imagery data, which not only disentangles the impacts of genotype-specific stomatal traits and environmental conditions but also enables the prediction of gs in new environments. The methodology involved using simulated thermal imagery data generated from a 3D biophysical model to train a machine learning model that could be applied to real thermal images to predict stomatal model parameters and gs itself. The method was evaluated by comparing predictions against manual gs measurements, all of which were not part of the model training process, as the model was trained against only simulated images. When compared against manual gs measurements using a porometer, the prediction R2 was 0.7, which is likely comparable to the accuracy of the manual porometer-based gs measurements (relative to a leaf gas exchange system). The developed pipeline enables high-throughput gs model parameter calibration and gs estimation.<\/jats:p>","DOI":"10.1093\/jxb\/eraf420","type":"journal-article","created":{"date-parts":[[2025,9,18]],"date-time":"2025-09-18T11:46:56Z","timestamp":1758196016000},"page":"312-329","source":"Crossref","is-referenced-by-count":7,"title":["Automated calibration of stomatal conductance models from thermal imagery by leveraging synthetic images generated from Helios 3D biophysical model simulations"],"prefix":"10.1093","volume":"77","author":[{"given":"Ismael K","family":"Mayanja","sequence":"first","affiliation":[{"name":"Department of Biological and Agricultural Engineering, University of California , Davis, CA 95616 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heesup","family":"Yun","sequence":"additional","affiliation":[{"name":"Department of Biological and Agricultural Engineering, University of California , Davis, CA 95616 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1919-2324","authenticated-orcid":false,"given":"Brian N","family":"Bailey","sequence":"additional","affiliation":[{"name":"Department of Plant Sciences, University of California , Davis, CA 95616 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,9,19]]},"reference":[{"key":"2026011209070639100_eraf420-B1","doi-asserted-by":"crossref","first-page":"diz007","DOI":"10.1093\/insilicoplants\/diz007","article-title":"HydroShoot: a functional-structural plant model for simulating hydraulic structure, gas and energy exchange dynamics of complex plant canopies under water deficit\u2014application to grapevine (Vitis vinifera)","volume":"1","author":"Albasha","year":"2019","journal-title":"in silico Plants"},{"key":"2026011209070639100_eraf420-B2","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1016\/j.ecolmodel.2017.11.022","article-title":"A reverse ray-tracing method for modelling the net radiative flux in leaf-resolving plant canopy simulations","volume":"368","author":"Bailey","year":"2018","journal-title":"Ecological Modelling"},{"key":"2026011209070639100_eraf420-B3","doi-asserted-by":"crossref","first-page":"1185","DOI":"10.3389\/fpls.2019.01185","article-title":"Helios: a scalable 3D plant and environmental biophysical modeling framework","volume":"10","author":"Bailey","year":"2019","journal-title":"Frontiers in Plant Science"},{"key":"2026011209070639100_eraf420-B4","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1007\/978-94-017-0519-6_48","volume-title":"Progress in photosynthesis research.","author":"Ball","year":"1987"},{"key":"2026011209070639100_eraf420-B5","doi-asserted-by":"crossref","first-page":"2380","DOI":"10.1016\/j.rse.2009.06.018","article-title":"Mapping canopy conductance and CWSI in olive orchards using high resolution thermal remote sensing imagery","volume":"113","author":"Berni","year":"2009","journal-title":"Remote Sensing of Environment"},{"key":"2026011209070639100_eraf420-B6","doi-asserted-by":"crossref","first-page":"2183","DOI":"10.1016\/j.agrformet.2009.10.003","article-title":"Automated measurement of canopy stomatal conductance based on infrared temperature","volume":"149","author":"Blonquist","year":"2009","journal-title":"Agricultural and Forest Meteorology"},{"key":"2026011209070639100_eraf420-B7","first-page":"216","article-title":"A survey on multi-output regression","volume":"5","author":"Borchani","year":"2015","journal-title":"Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery"},{"key":"2026011209070639100_eraf420-B8","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1023\/A:1010933404324","article-title":"Random forests","volume":"45","author":"Breiman","year":"2001","journal-title":"Machine Learning"},{"key":"2026011209070639100_eraf420-B9","doi-asserted-by":"crossref","first-page":"1767","DOI":"10.1046\/j.1365-3040.2003.01094.x","article-title":"A hydromechanical and biochemical model of stomatal conductance","volume":"26","author":"Buckley","year":"2003","journal-title":"Plant, Cell & Environment"},{"key":"2026011209070639100_eraf420-B10","doi-asserted-by":"crossref","first-page":"1647","DOI":"10.1111\/j.1365-3040.2012.02515.x","article-title":"Simple models for stomatal conductance derived from a process model: cross-validation against sap flux data","volume":"35","author":"Buckley","year":"2012","journal-title":"Plant, Cell & Environment"},{"key":"2026011209070639100_eraf420-B11","doi-asserted-by":"crossref","first-page":"572","DOI":"10.1104\/pp.16.01772","article-title":"Modeling stomatal conductance","volume":"174","author":"Buckley","year":"2017","journal-title":"Plant Physiology"},{"key":"2026011209070639100_eraf420-B12","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1111\/nph.15899","article-title":"How do stomata respond to water status?","volume":"224","author":"Buckley","year":"2019","journal-title":"New Phytologist"},{"key":"2026011209070639100_eraf420-B13","volume-title":"An introduction to environmental biophysics","author":"Campbell","year":"2000"},{"key":"2026011209070639100_eraf420-B14","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1071\/PP9920519","article-title":"Coupled photosynthesis\u2013stomatal conductance model for leaves of C4 plants","volume":"19","author":"Collatz","year":"1992","journal-title":"Functional Plant Biology"},{"key":"2026011209070639100_eraf420-B15","first-page":"1419","article-title":"An overview of models of stomatal conductance at the leaf level","volume":"33","author":"Damour","year":"2010","journal-title":"Plant, Cell & Environment"},{"key":"2026011209070639100_eraf420-B16","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1007\/BF00386231","article-title":"A biochemical model of photosynthetic CO2 assimilation in leaves of C3 species","volume":"149","author":"Farquhar","year":"1980","journal-title":"Planta"},{"key":"2026011209070639100_eraf420-B17","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1146\/annurev.pp.33.060182.001533","article-title":"Stomatal conductance and photosynthesis","volume":"33","author":"Farquhar","year":"1982","journal-title":"Annual Review of Plant Physiology"},{"key":"2026011209070639100_eraf420-B18","first-page":"191","article-title":"An empirical model of stomatal conductance","volume":"11","author":"Farquhar","year":"1984","journal-title":"Functional Plant Biology"},{"key":"2026011209070639100_eraf420-B19","doi-asserted-by":"crossref","first-page":"S-85","DOI":"10.2135\/cropsci2009.10.0564","article-title":"Breeding and cereal yield progress","volume":"50","author":"Fischer","year":"2010","journal-title":"Crop Science"},{"key":"2026011209070639100_eraf420-B20","doi-asserted-by":"crossref","first-page":"10343","DOI":"10.1073\/pnas.0904209106","article-title":"Maximum leaf conductance driven by CO2 effects on stomatal size and density over geologic time","volume":"106","author":"Franks","year":"2009","journal-title":"Proceedings of the National Academy of Sciences, USA"},{"key":"2026011209070639100_eraf420-B21","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1146\/annurev.pp.19.060168.001235","article-title":"Transpiration and leaf temperature","volume":"19","author":"Gates","year":"1968","journal-title":"Annual Review of Plant Physiology"},{"key":"2026011209070639100_eraf420-B22","volume-title":"Photosynthesis, 6th edn","author":"Hall","year":"1999"},{"key":"2026011209070639100_eraf420-B23","doi-asserted-by":"crossref","first-page":"2185","DOI":"10.1093\/jxb\/erq095","article-title":"Adapting APSIM to model the physiology and genetics of complex adaptive traits in field crops","volume":"61","author":"Hammer","year":"2010","journal-title":"Journal of Experimental Botany"},{"key":"2026011209070639100_eraf420-B24","doi-asserted-by":"crossref","first-page":"108423","DOI":"10.1016\/j.agrformet.2021.108423","article-title":"Machine learning produces higher prediction accuracy than the Jarvis-type model of climatic control on stomatal conductance in a dryland wheat agro-ecosystem","volume":"304","author":"Houshmandfar","year":"2021","journal-title":"Agricultural and Forest Meteorology"},{"key":"2026011209070639100_eraf420-B25","doi-asserted-by":"crossref","first-page":"1129","DOI":"10.1111\/tpj.13827","article-title":"A multi-parent advanced generation inter-cross (MAGIC) population for genetic analysis and improvement of cowpea (Vigna unguiculata L)","volume":"93","author":"Huynh","year":"2018","journal-title":"The Plant Journal"},{"key":"2026011209070639100_eraf420-B26","volume-title":"An introduction to solar radiation","author":"Iqbal","year":"2012"},{"key":"2026011209070639100_eraf420-B27","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1080\/1343943X.2019.1625273","article-title":"A new indicator of leaf stomatal conductance based on thermal imaging for field grown cowpea","volume":"23","author":"Iseki","year":"2020","journal-title":"Plant Production Science"},{"key":"2026011209070639100_eraf420-B28","doi-asserted-by":"crossref","first-page":"910","DOI":"10.1109\/9.855552","article-title":"Gaussian filters for nonlinear filtering problems","volume":"45","author":"Ito","year":"2000","journal-title":"IEEE Transactions on Automatic Control"},{"key":"2026011209070639100_eraf420-B29","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1007\/BF00296705","article-title":"A reexamination of the crop water stress index","volume":"9","author":"Jackson","year":"1988","journal-title":"Irrigation Science"},{"key":"2026011209070639100_eraf420-B30","doi-asserted-by":"crossref","first-page":"23418","DOI":"10.1038\/srep23418","article-title":"Impact of the representation of stomatal conductance on model projections of heatwave intensity","volume":"6","author":"Kala","year":"2016","journal-title":"Scientific Reports"},{"key":"2026011209070639100_eraf420-B31","doi-asserted-by":"crossref","DOI":"10.1007\/978-0-387-78341-3","volume-title":"Plant physiological ecology","author":"Lambers","year":"2008"},{"key":"2026011209070639100_eraf420-B32","doi-asserted-by":"crossref","first-page":"468","DOI":"10.1111\/ppl.12530","article-title":"Factors influencing stomatal conductance in response to water availability in grapevine: a meta-analysis","volume":"159","author":"Lavoie-Lamoureux","year":"2017","journal-title":"Physiologia Plantarum"},{"key":"2026011209070639100_eraf420-B33","doi-asserted-by":"crossref","first-page":"781","DOI":"10.1146\/annurev-arplant-042817-040305","article-title":"Water use efficiency as a constraint and target for improving the resilience and productivity of C3 and C4 crops","volume":"70","author":"Leakey","year":"2019","journal-title":"Annual Review of Plant Biology"},{"key":"2026011209070639100_eraf420-B34","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1109\/IWFHR.2002.1030917","volume-title":"Proceedings of the Eighth International Workshop on Frontiers in Handwriting Recognition","author":"Leedham","year":"2002"},{"key":"2026011209070639100_eraf420-B35","doi-asserted-by":"crossref","first-page":"0189","DOI":"10.34133\/plantphenomics.0189","article-title":"Simulation of automatically annotated visible and multi-\/hyperspectral images using the Helios 3D plant and radiative transfer modeling framework","volume":"6","author":"Lei","year":"2024","journal-title":"Plant Phenomics"},{"key":"2026011209070639100_eraf420-B36","doi-asserted-by":"crossref","first-page":"1682341","DOI":"10.1080\/15592324.2019.1682341","article-title":"Seasonal change in response of stomatal conductance to vapor pressure deficit and three phytohormones in three tree species","volume":"14","author":"Li","year":"2019","journal-title":"Plant Signaling & Behavior"},{"key":"2026011209070639100_eraf420-B37","doi-asserted-by":"crossref","first-page":"4313","DOI":"10.5194\/gmd-15-4313-2022","article-title":"Implementation and evaluation of the unified stomatal optimization approach in the functionally assembled terrestrial ecosystem simulator (FATES)","volume":"15","author":"Li","year":"2022","journal-title":"Geoscientific Model Development"},{"key":"2026011209070639100_eraf420-B38","doi-asserted-by":"crossref","first-page":"2674","DOI":"10.3390\/s18082674","article-title":"Machine learning in agriculture: a review","volume":"18","author":"Liakos","year":"2018","journal-title":"Sensors"},{"key":"2026011209070639100_eraf420-B39","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1007\/s11120-020-00797-w","article-title":"A process-based coupled model of stomatal conductance\u2013photosynthesis\u2013transpiration during leaf ontogeny for water-saving irrigated rice","volume":"147","author":"Lv","year":"2021","journal-title":"Photosynthesis Research"},{"key":"2026011209070639100_eraf420-B40","doi-asserted-by":"crossref","first-page":"0169","DOI":"10.34133\/plantphenomics.0169","article-title":"Practical considerations and limitations of using leaf and canopy temperature measurements as a stomatal conductance proxy: sensitivity across environmental conditions, scale, and sample size","volume":"6","author":"Mayanja","year":"2024","journal-title":"Plant Phenomics"},{"key":"2026011209070639100_eraf420-B41","doi-asserted-by":"crossref","first-page":"1538","DOI":"10.21273\/HORTSCI.25.12.1538","article-title":"Sources of error in the estimation of stomatal conductance and transpiration from porometer data","volume":"25","author":"McDermitt","year":"1990","journal-title":"HortScience"},{"key":"2026011209070639100_eraf420-B42","doi-asserted-by":"crossref","first-page":"2134","DOI":"10.1111\/j.1365-2486.2010.02375.x","article-title":"Reconciling the optimal and empirical approaches to modelling stomatal conductance","volume":"17","author":"Medlyn","year":"2011","journal-title":"Global Change Biology"},{"key":"2026011209070639100_eraf420-B43","first-page":"15","volume-title":"Physiological breeding II: a field guide to wheat phenotyping","author":"Pietragalla","year":"2012"},{"key":"2026011209070639100_eraf420-B44","doi-asserted-by":"crossref","first-page":"108825","DOI":"10.1016\/j.scienta.2019.108825","article-title":"Sensitivity analysis of four crop water stress indices to ambient environmental conditions and stomatal conductance","volume":"259","author":"Poirier-Pocovi","year":"2020","journal-title":"Scientia Horticulturae"},{"key":"2026011209070639100_eraf420-B45","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1071\/BT9690081","article-title":"Stomatal ontogeny of the vegetative and floral organs of some Papilionaceae","volume":"17","author":"Shah","year":"1969","journal-title":"Australian Journal of Botany"},{"key":"2026011209070639100_eraf420-B46","doi-asserted-by":"crossref","first-page":"3182","DOI":"10.3390\/rs12193182","article-title":"Hyperspectral and thermal sensing of stomatal conductance, transpiration, and photosynthesis for soybean and maize under drought","volume":"12","author":"Sobejano-Paz","year":"2020","journal-title":"Remote Sensing"},{"key":"2026011209070639100_eraf420-B47","doi-asserted-by":"crossref","DOI":"10.1201\/b10675","volume-title":"Ray tracing from the ground up","author":"Suffern","year":"2016"},{"key":"2026011209070639100_eraf420-B48","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1007\/s40626-019-00161-x","article-title":"Contrasting leaf porometer and infra-red gas analyser methodologies: an old paradigm about the stomatal conductance measurement","volume":"31","author":"Toro","year":"2019","journal-title":"Theoretical and Experimental Plant Physiology"},{"key":"2026011209070639100_eraf420-B49","doi-asserted-by":"crossref","first-page":"2839","DOI":"10.1093\/jxb\/erz068","article-title":"Dynamic leaf energy balance: deriving stomatal conductance from thermal imaging in a dynamic environment","volume":"70","author":"Vialet-Chabrand","year":"2019","journal-title":"Journal of Experimental Botany"},{"key":"2026011209070639100_eraf420-B50","doi-asserted-by":"crossref","first-page":"2213","DOI":"10.3390\/rs12142213","article-title":"Random forest algorithm improves detection of physiological activity embedded within reflectance spectra using stomatal conductance as a test case","volume":"12","author":"Vitrack-Tamam","year":"2020","journal-title":"Remote Sensing"},{"key":"2026011209070639100_eraf420-B51","author":"Wada","year":"2016"},{"key":"2026011209070639100_eraf420-B52","doi-asserted-by":"crossref","first-page":"13","DOI":"10.5194\/bg-18-13-2021","article-title":"Calculating canopy stomatal conductance from eddy covariance measurements, in light of the energy budget closure problem","volume":"18","author":"Wehr","year":"2021","journal-title":"Biogeosciences"},{"key":"2026011209070639100_eraf420-B53","first-page":"5470","volume-title":"Proceedings of the IEEE\/CVF Conference on Computer Vision and Pattern Recognition","author":"Yun","year":"2024"},{"key":"2026011209070639100_eraf420-B54","doi-asserted-by":"crossref","first-page":"109278","DOI":"10.1016\/j.ecolind.2022.109278","article-title":"Comparison of various approaches for estimating leaf water content and stomatal conductance in different plant species using hyperspectral data","volume":"142","author":"Zhang","year":"2022","journal-title":"Ecological Indicators"},{"key":"2026011209070639100_eraf420-B55","first-page":"98","volume-title":"Autonomous air and ground sensing systems for agricultural optimization and phenotyping VI. Proceedings Vol 11747","author":"Zhao","year":"2021"},{"key":"2026011209070639100_eraf420-B56","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1016\/S0168-1923(03)00108-4","article-title":"Modeling of the short-wave radiation distribution in an agroforestry system","volume":"118","author":"Zhao","year":"2003","journal-title":"Agricultural and Forest Meteorology"},{"key":"2026011209070639100_eraf420-B57","doi-asserted-by":"publisher","DOI":"10.1029\/2005WR004581","article-title":"Modeling of long-wave and net radiation energy distribution within a homogeneous plant canopy via multiple scattering processes","volume":"42","author":"Zhao","year":"2006","journal-title":"Water Resources Research"},{"key":"2026011209070639100_eraf420-B58","doi-asserted-by":"crossref","first-page":"833","DOI":"10.1093\/aob\/mcx141","article-title":"A 3-D functional\u2013structural grapevine model that couples the dynamics of water transport with leaf gas exchange","volume":"121","author":"Zhu","year":"2018","journal-title":"Annals of Botany"}],"container-title":["Journal of Experimental Botany"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/jxb\/advance-article-pdf\/doi\/10.1093\/jxb\/eraf420\/64324609\/eraf420.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/jxb\/article-pdf\/77\/2\/312\/64324609\/eraf420.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/jxb\/article-pdf\/77\/2\/312\/64324609\/eraf420.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,12]],"date-time":"2026-01-12T14:07:22Z","timestamp":1768226842000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/jxb\/article\/77\/2\/312\/8258535"}},"subtitle":[],"editor":[{"given":"Johannes","family":"Kromdijk","sequence":"additional","affiliation":[{"name":"University of Cambridge ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2025,9,19]]},"references-count":58,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2025,9,19]]},"published-print":{"date-parts":[[2026,1,12]]}},"URL":"https:\/\/doi.org\/10.1093\/jxb\/eraf420","relation":{},"ISSN":["0022-0957","1460-2431"],"issn-type":[{"value":"0022-0957","type":"print"},{"value":"1460-2431","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,1,12]]},"published":{"date-parts":[[2025,9,19]]}}}