{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,20]],"date-time":"2026-01-20T11:17:45Z","timestamp":1768907865627,"version":"3.49.0"},"reference-count":72,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2014,12,22]],"date-time":"2014-12-22T00:00:00Z","timestamp":1419206400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Remote Sensing"],"abstract":"<jats:p>A passive method for remote sensing of the nuisance green algae Cladophora glomerata in rivers is presented using an unmanned aerial vehicle (UAV). Included are methods for UAV operation, lens distortion correction, image georeferencing, and spectral analysis to support algal cover mapping. Eighteen aerial photography missions were conducted over the summer of 2013 using an off-the-shelf UAV and three-band,  wide-angle, red, green, and blue (RGB) digital camera sensor. Images were post-processed, mosaicked, and georeferenced so automated classification and mapping could be completed. An adaptive cosine estimator (ACE) and spectral angle mapper (SAM) algorithm were used to complete the algal identification. Digital analysis of optical imagery correctly identified filamentous algae and background coverage 90% and 92% of the time, and tau coefficients were 0.82 and 0.84 for ACE and SAM, respectively. Thereafter, algal cover was characterized for a one-kilometer channel segment during each of the 18 UAV flights. Percent cover ranged from &lt;5% to &gt;50%, and increased immediately after vernal freshet, peaked in midsummer, and declined in the fall. Results indicate that optical remote sensing with UAV holds promise for completing spatially precise, and multi-temporal measurements of algae or submerged aquatic vegetation in shallow rivers with low turbidity and good optical transmission.<\/jats:p>","DOI":"10.3390\/rs61212815","type":"journal-article","created":{"date-parts":[[2014,12,22]],"date-time":"2014-12-22T08:31:01Z","timestamp":1419237061000},"page":"12815-12836","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":127,"title":["Remote Sensing of Submerged Aquatic Vegetation in a Shallow Non-Turbid River Using an Unmanned Aerial Vehicle"],"prefix":"10.3390","volume":"6","author":[{"given":"Kyle","family":"Flynn","sequence":"first","affiliation":[{"name":"Civil and Environmental Engineering Department, Tufts University, Medford, MA 02155, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0238-6376","authenticated-orcid":false,"given":"Steven","family":"Chapra","sequence":"additional","affiliation":[{"name":"Civil and Environmental Engineering Department, Tufts University, Medford, MA 02155, USA"}]}],"member":"1968","published-online":{"date-parts":[[2014,12,22]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"86","DOI":"10.2307\/1311969","article-title":"Assessing water quality with submersed aquatic vegetation","volume":"43","author":"Dennison","year":"1993","journal-title":"BioScience"},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Carbonneau, P.E., and Pi\u00e9gay, H. (2012). Fluvial Remote Sensing for Science and Management, John Wiley & Sons, Ltd.","DOI":"10.1002\/9781119940791"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1016\/0304-3770(86)90031-8","article-title":"Effects of submersed macrophytes on ecosystem processes","volume":"26","author":"Carpenter","year":"1986","journal-title":"Aquat. Bot."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Ziglio, G., Siligardi, M., and Flaim, G. (2006). Biological Monitoring of Rivers, John Wiley & Sons, Ltd.","DOI":"10.1002\/0470863781"},{"key":"ref_5","unstructured":"Ohrel, R.L., and Registar, K.M. (2006). Submerged aquatic vegetation, Volunteer Estuary Monitoring: A Methods Manual."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1080\/00785236.1995.10422039","article-title":"Submerged aquatic vegetation in relation to different nutrient regimes","volume":"41","author":"Duarte","year":"1995","journal-title":"Ophelia"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"106","DOI":"10.3176\/eco.2012.2.03","article-title":"Response of submerged aquatic vegetation to eutrophication-related environment descriptors in coastal waters of the NE Baltic Sea","volume":"61","author":"Torn","year":"2012","journal-title":"Est. J. Ecol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1007\/BF02872474","article-title":"The ecology of river algae","volume":"22","author":"Blum","year":"1956","journal-title":"Bot. Rev."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1016\/0043-1354(70)90061-8","article-title":"Biology of Cladophora in freshwaters","volume":"4","author":"Whitton","year":"1970","journal-title":"Water Res."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1111\/j.0022-3646.1992.00415.x","article-title":"The ecology of Cladophora","volume":"28","author":"Dodds","year":"1992","journal-title":"J. Phycol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1119","DOI":"10.1046\/j.1365-3040.2000.00596.x","article-title":"Strategies providing success in a variable habitat: I. Relationships of environmental factors and dominance of Cladophora glomerata","volume":"23","author":"Ensminger","year":"2000","journal-title":"Plant Cell Environ."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"839","DOI":"10.1111\/j.1529-8817.2008.00538.x","article-title":"An ecological review of Cladophora glomerata (Chlorophyta) in the Lauerentian Great Lakes","volume":"44","author":"Higgins","year":"2008","journal-title":"J. Phycol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1016\/j.jglr.2010.03.001","article-title":"Great Lakes Cladophora in the 21st century: Same algae-different ecosystem","volume":"36","author":"Auer","year":"2010","journal-title":"J. Great Lakes Res."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1007\/BF00008320","article-title":"The role of nitrogen and phosphorus in the development of Cladophora glomerata (L.) Kutzing in the Manawatu River, New Zealand","volume":"131","author":"Freeman","year":"1986","journal-title":"Hydrobiologia"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1007\/BF00006968","article-title":"Nuisance biomass levels of periphytic algae in streams","volume":"157","author":"Welch","year":"1988","journal-title":"Hydrobiologia"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1021\/es801217q","article-title":"Eutrophication of U.S. freshwaters: Analysis of potential economic damages","volume":"43","author":"Dodds","year":"2009","journal-title":"Environ. Sci. Technol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1080\/00288330.1987.9516214","article-title":"A survey of filamentous algal proliferations in New Zealand rivers","volume":"21","author":"Biggs","year":"1987","journal-title":"New Zeal. J. Mar. Fresh."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1016\/0034-4257(75)90004-8","article-title":"Analysis of Cladophora distribution in Lake Ontario using remote sensing","volume":"4","author":"Wezernak","year":"1975","journal-title":"Remote Sens. Environ."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1016\/S0380-1330(82)71952-5","article-title":"The use of remote sensing to map the areal distribution of Cladophora glomerata at a site in Lake Huron","volume":"8","author":"Lekan","year":"1982","journal-title":"J. Great Lakes Res."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1016\/j.jglr.2013.05.006","article-title":"Mapping and monitoring the extent of submerged aquatic vegetation in the Laurentian Great Lakes with multi-scale satellite remote sensing","volume":"39","author":"Shuchman","year":"2013","journal-title":"J. Great Lakes Res."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Vahtm\u00e4e, E., and Kutser, T. (2007). Mapping bottom type and water depth in shallow coastal waters with satellite remote sensing. J. Coast. Res., 185\u2013189.","DOI":"10.2112\/JCR-SI50-036.1"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"122","DOI":"10.3394\/0380-1330(2007)33[122:QOHCOS]2.0.CO;2","article-title":"Quantification of historical changes of submerged aquatic vegetation cover in two bays of Lake Ontario with three complementary methods","volume":"33","author":"Zhu","year":"2007","journal-title":"J. Great Lakes Res."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"693","DOI":"10.4319\/lom.2009.7.693","article-title":"Detection and characterization of benthic filamentous algal stands (Cladophora sp.) on rocky substrata using a high-frequency echosounder","volume":"7","author":"Depew","year":"2009","journal-title":"Limnol. Oceanog-Meth."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1002\/esp.1637","article-title":"Optical remote mapping of rivers at sub-meter resolutions and watershed extents","volume":"33","author":"Marcus","year":"2008","journal-title":"Earth Surf. Process. Landf."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"925","DOI":"10.1002\/rra.2700","article-title":"Application of aerial digital photography for macrophyte cover and composition survey in small rural streams","volume":"30","author":"Anker","year":"2013","journal-title":"River Res. Applic."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Carbonneau, P.E., and Pi\u00e9gay, H. (2012). Fluvial Remote Sensing for Science and Management, John Wiley & Sons, Ltd.","DOI":"10.1002\/9781119940791"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1007\/s10661-007-9855-3","article-title":"Remote sensing of aquatic vegetation: Theory and applications","volume":"140","author":"Silva","year":"2008","journal-title":"Environ. Monit. Assess."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1867","DOI":"10.1002\/esp.2094","article-title":"Remote sensing of rivers: The emergence of a subdiscipline in the river sciences","volume":"35","author":"Marcus","year":"2010","journal-title":"Earth Surf. Process. Landf."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1002\/ppp.437","article-title":"Mapping of periglacial geomorphology using kite\/balloon aerial photography","volume":"14","author":"Boike","year":"2003","journal-title":"Paermafrost Periglac. Process."},{"key":"ref_30","first-page":"1781","article-title":"Low-cost aerial photography for high-resolution mapping of hydrothermal areas in Yellowstone National Park","volume":"29","author":"Becker","year":"2007","journal-title":"Int. J. Remote Sens."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1109\/TGRS.2008.2010457","article-title":"Thermal and narrowband multispectral remote sensing for vegetation monitoring from an unmanned aerial vehicle","volume":"47","author":"Berni","year":"2009","journal-title":"IEEE Trans. Geosci. Remote Sens."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1006\/jema.1998.0255","article-title":"The cost-effectiveness of remote sensing for tropical coastal resources assessment and management","volume":"55","author":"Mumby","year":"1999","journal-title":"J. Environ. Manag."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pone.0038882","article-title":"Estimating distribution of hidden objects with drones: From tennis balls to manatees","volume":"7","author":"Martin","year":"2012","journal-title":"PLoS One"},{"key":"ref_34","unstructured":"Zang, W., Lin, J., Wang, Y., and Tao, H. (2012). World Automation Congress (WAC), Institute of Electrical and Electronics Engineers (IEEE)."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1671","DOI":"10.3390\/rs4061671","article-title":"Unmanned aircraft systems in remote sensing and scientific research: Classification and considerations of use","volume":"4","author":"Watts","year":"2012","journal-title":"Remote Sens."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/j.isprsjprs.2014.02.013","article-title":"Unmanned aerial systems for photogrammetry and remote sensing: A review","volume":"92","author":"Colomina","year":"2014","journal-title":"ISPRS J. Photogramm. Remote Sens."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1111\/j.1749-8198.2010.00381.x","article-title":"Small-scale remotely piloted vehicles in environmental research","volume":"4","author":"Hardin","year":"2010","journal-title":"Geog. Comp."},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Carbonneau, P.E., and Pi\u00e9gay, H. (2012). Fluvial Remote Sensing for Science and Management, John Wiley & Sons, Ltd.","DOI":"10.1002\/9781119940791"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1","DOI":"10.2747\/1548-1603.48.1.1","article-title":"Introduction\u2014Small-scale unmanned aerial systems for environmental remote sensing","volume":"48","author":"Hardin","year":"2011","journal-title":"GISci. Remote Sens."},{"key":"ref_40","unstructured":"Federal Aviation Adminstration (FAA) (2007). Unmanned Aircraft Operations in the National Airspace System."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"709","DOI":"10.1109\/TGRS.2008.2009763","article-title":"Investigation of fish-eye lenses for small-UAV aerial photography","volume":"47","author":"Gurtner","year":"2009","journal-title":"IEEE Trans. Geosci. Remote Sens."},{"key":"ref_42","unstructured":"Leighton, J. (2010). System Design of an Unmanned Aerial Vehicle (UAV) for Marine Environmental Sensing. [Master\u2019s Thesis, Massachusetts Institute of Technology]."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"1117","DOI":"10.1130\/0016-7606(1952)63[1117:HAAOET]2.0.CO;2","article-title":"Hypsometric (area-altitude) analysis of erosional topography","volume":"63","author":"Strahler","year":"1952","journal-title":"Geol. Soc. Am. Bull."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1111\/j.0022-3646.1992.00443.x","article-title":"Physiological indicators of nutrient deficiency in Cladophora (Chlorophyta) in the Clark Fork of the Colubmia River, Montana","volume":"28","author":"Lohman","year":"1992","journal-title":"J. Phycol."},{"key":"ref_45","first-page":"17","article-title":"Monitoring algae levels in the Clark Fork River","volume":"2","author":"Watson","year":"1996","journal-title":"Intermt. J. Sci."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"1008","DOI":"10.1111\/j.1752-1688.2012.00666.x","article-title":"Response of algal biomass to large-scale nutrient controls in the Clark Fork River, Montana, United States","volume":"48","author":"Suplee","year":"2012","journal-title":"J. Am. Water Resour. As."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"99","DOI":"10.2747\/1548-1603.48.1.99","article-title":"Small-scale unmanned aerial vehicles in environmental remote sensing: Challenges and opportunities","volume":"48","author":"Hardin","year":"2011","journal-title":"GISci. Remote Sens."},{"key":"ref_48","unstructured":"Edwards, T.K., and Glysson, G.D. (1999). Applications of Hydraulics, Department of the Interior, U.S. Geological Survey."},{"key":"ref_49","unstructured":"American Public Health Association (APHA) (1981). Standard Methods for the Examination of Water and Wastewater."},{"key":"ref_50","unstructured":"National Water Information System Data\u2014World Wide Web (Water Data for the Nation), Available online: http:\/\/waterdata.usgs.gov\/nwis\/."},{"key":"ref_51","first-page":"680","article-title":"Solar altitude nomograms","volume":"31","author":"Fleming","year":"1965","journal-title":"Photogramm. Eng."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"1407","DOI":"10.14358\/PERS.71.12.1407","article-title":"Acquisition of through-water aerial survey images: Surface effects and the prediction of sun glitter and subsurface illumination","volume":"71","author":"Mount","year":"2005","journal-title":"Photogramm. Eng. Remote Sens."},{"key":"ref_53","unstructured":"Gardner, S. Personal communication."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"977","DOI":"10.1016\/S0262-8856(03)00137-9","article-title":"Image registration methods: A survey","volume":"21","author":"Flusser","year":"2003","journal-title":"Image Vision Comput."},{"key":"ref_55","unstructured":"DJI Innovations, Inc. PHANTOM Quick Start Manual v1.6 2013.05.28 Revision for Naza-M Firmware v3.12 & Assistant Software v2.12. Available online: www.dji-innovations.com\/."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"1335","DOI":"10.1109\/TPAMI.2006.153","article-title":"A generic camera model and calibration method for conventional, wide-angle, and fish-eye lenses","volume":"28","author":"Kannala","year":"2006","journal-title":"IEEE Trans. Pattern. Anal. Mach. Intell."},{"key":"ref_57","unstructured":"Bouguet, J.-Y. (2013). Camera Calibration toolbox for Matlab\u00ae, California Institute of Technology Computer Vision Research Group."},{"key":"ref_58","unstructured":"(Matlab R2007b, 2013). Matlab R2007b."},{"key":"ref_59","unstructured":"(2013). ArcGIS 10.0 User\u2019s Manual, ESRI (Environmental Systems Resource Institute)."},{"key":"ref_60","unstructured":"(Opticks 4.11.0, 2013). Opticks 4.11.0."},{"key":"ref_61","first-page":"435","article-title":"Tau coefficients for accuracy assessment of classification of remote sensing data","volume":"62","author":"Ma","year":"1995","journal-title":"Photogramm. Eng. Remote Sens."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1007\/s002270050238","article-title":"Coral reef habitat mapping: How much detail can remote sensing provide?","volume":"130","author":"Mumby","year":"1997","journal-title":"Mar. Biol."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1016\/0034-4257(91)90048-B","article-title":"A review of assessing the accuracy of classifications of remotely sensed data","volume":"37","author":"Congalton","year":"1991","journal-title":"Remote Sens. Environ."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"329","DOI":"10.3176\/biol.ecol.2006.4.05","article-title":"Spectral library of macroalgae and benthic substrates in Estonian coastal waters","volume":"55","author":"Kutser","year":"2006","journal-title":"Proc. Estonian Acad. Sci. Biol. Ecol"},{"key":"ref_65","unstructured":"Tanis, F.J. (1980). A Remote Sensing Technique to Monitor Cladophora in the Great Lakes."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"4034","DOI":"10.1016\/j.rse.2008.01.022","article-title":"Identification of invasive vegetation using hyperspectral remote sensing in the California Delta ecosystem","volume":"112","author":"Hestir","year":"2008","journal-title":"Remote Sens. Environ."},{"key":"ref_67","unstructured":"Stevenson, R.J., Bothwell, M.L., and Lowe, R.L. (1996). Algal Ecology: Freshwater Bethic Ecosystems, Academic Press."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1002\/(SICI)1099-1646(199603)12:2\/3<131::AID-RRR385>3.0.CO;2-X","article-title":"Hydraulic habitat of plants in streams","volume":"12","author":"Biggs","year":"1996","journal-title":"Regul. River."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1002\/(SICI)1099-1646(199603)12:2\/3<251::AID-RRR393>3.0.CO;2-X","article-title":"Hydraulic habitat suitability for periphyton in rivers","volume":"12","author":"Biggs","year":"1996","journal-title":"Regul. River."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"1320","DOI":"10.1002\/rra.1244","article-title":"Effects of pulsed flows on nuisance periphyton growths in rivers: A mesocosm study","volume":"25","author":"Flinders","year":"2009","journal-title":"River Res. Applic."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1111\/j.0022-3646.1995.00233.x","article-title":"Disturbance of stream periphyton by perturbations in shear stress: Time to structural failure and differences in community resistance","volume":"31","author":"Biggs","year":"1995","journal-title":"J. Phycol."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"614","DOI":"10.1899\/09-059.1","article-title":"Spatial patterns in periphyton biomass after low-magnitude flow spates: Geomorphic factors affecting patchiness across Gravel\u2013Cobble Riffles","volume":"29","author":"Luce","year":"2010","journal-title":"J. N. Am. Benthol. Soc."}],"container-title":["Remote Sensing"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2072-4292\/6\/12\/12815\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T21:11:26Z","timestamp":1760217086000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2072-4292\/6\/12\/12815"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,12,22]]},"references-count":72,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2014,12]]}},"alternative-id":["rs61212815"],"URL":"https:\/\/doi.org\/10.3390\/rs61212815","relation":{},"ISSN":["2072-4292"],"issn-type":[{"value":"2072-4292","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,12,22]]}}}