Phenopix: A R package for image-based vegetation phenology

Agricultural and Forest Meteorology

Volumn 220, Issue , 2016, Pages 141-150

  Filippa, Gianluca ^a   Cremonese, Edoardo ^a   Migliavacca, Mirco ^b   Galvagno, Marta ^a   Forkel, Matthias ^b,f   Wingate, Lisa ^c   Tomelleri, Enrico ^d   Morra di Cella, Umberto ^a   Richardson, Andrew D ^e  

^a Climate Change Unit   (Italy)

^b MAX PLANCK INSTITUTE FOR BIOGEOCHEMISTRY   (Germany)

^c BORDEAUX SCIENCES AGRO   (France)

^d INSTITUTE FOR RENEWABLE ENERGY   (Italy)

^e HARVARD UNIVERSITY   (United States)

^f Geoinformation Research Group Remote Sensing   (Austria)

Author keywords

Community ecology; Image analysis; Phenology; Pixel based analysis

Indexed keywords

COMMUNITY ECOLOGY; DATA PROCESSING; DECIDUOUS FOREST; DIGITAL IMAGE; GRASSLAND; IMAGE ANALYSIS; PHENOLOGY; PIXEL; SOFTWARE; SUBALPINE ENVIRONMENT; TEMPERATE FOREST; THRESHOLD; TRAJECTORY; TROPICAL REGION; UNCERTAINTY ANALYSIS; VEGETATION COVER;

EID: 84961386116     PISSN: 01681923     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.agrformet.2016.01.006     Document Type: Article

References (36)

1. Ahrends H.E., Brügger R., Stöckli R., Schenk J., Michna P., Jeanneret F., Wanner H., Eugster W. Quantitative phenological observations of a mixed beech forest in northern Switzerland with digital photography. J. Geophys. Res. 2008, 113:G04004. 10.1029/2007JG000650.
2. Beck P.S.A., Atzberger C., Høgda K.A., Johansen B., Skidmore A.K. Improved monitoring of vegetation dynamics at very high latitudes: a new method using MODIS NDVI. Remote Sens. Environ. 2006, 100:321-334. http://www.sciencedirect.com/science/article/pii/S0034425705003640. 10.1016/j.rse.2005.10.021.
3. Busetto L., Colombo R., Migliavacca M., Cremonese E., Meroni M., Galvagno M., Rossini M., Siniscalco C., Morra Di Cella U., Pari E. Remote sensing of larch phenological cycle and analysis of relationships with climate in the Alpine region. Glob. Change Biol. 2010, 10.1111/J.1365-2486.2010.02189.X.
4. Delbart N., Kergoat L., Toan T.L., Lhermitte J., Picard G. Determination of phenological dates in boreal regions using normalized difference water index. Remote Sens. Environ. 2005, 97:26-38. http://www.sciencedirect.com/science/article/pii/S0034425705001288. 10.1016/j.rse.2005.03.011.
5. Elmore A.J., Guinn S.M., Minsley B.J., Richardson A.D. Landscape controls on the timing of spring, autumn, and growing season length in mid-Atlantic forests. Glob. Change Biol. 2012, 18:656-674. 10.1111/j.1365-2486.2011.02521.x.
6. Filippa G., Cremonese E., Galvagno M., Migliavacca M., Morra di Cella U., Petey M., Siniscalco C. Five years of phenological monitoring in a mountain grassland: inter-annual patterns and evaluation of the sampling protocol. Int. J. Biometeorol. 2015, 10.1007/s00484-015-0999-5.
7. Forkel M., Migliavacca M., Thonicke K., Reichstein M., Schaphoff S., Weber U., Carvalhais N. Codominant water control on global interannual variability and trends in land surface phenology and greenness. Glob. Change Biol. 2015, 21:3414-3435. 10.1111/gcb.12950.
8. Galvagno M., Wohlfahrt G., Cremonese E., Rossini M., Colombo R., Filippa G., Julitta T., Manca G., Siniscalco C., Morra di Cella U., Migliavacca M. Phenology and carbon dioxide source/sink strength of a subalpine grassland in response to an exceptionally short snow season. Environ. Res. Lett. 2013, 8:025008.
9. Gillespie A.R., Kahle A.B., Walker R.E. Color enhancement of highly correlated images. II. Channel ratio and chromaticity transformation techniques. Remote Sens. Environ. 1987, 22:343-365.
10. Gu L., Post W., Baldocchi D., Black T., Suyker A., Verma S., Vesala T., Wofsy S. Characterizing the seasonal dynamics of plant community photosynthesis across a range of vegetation types. Phenology of Ecosystem Processes 2009, 35-58. Springer, New York, 10.1007/978-1-4419-0026-5_2. A. Noormets (Ed.).
11. Hartigan J.A., Wong M.A. Algorithm as 136: a k-means clustering algorithm. J. R. Stat. Soc. Ser. C (Appl. Stat.) 1979, 28:100-108. http://www.jstor.org/stable/2346830.
12. Hufkens K., Friedl M., Sonnentag O., Braswell B.H., Milliman T., Richardson A.D. Linking near-surface and satellite remote sensing measurements of deciduous broadleaf forest phenology. Remote Sens. Environ. 2012, 117:307-321. http://linkinghub.elsevier.com/retrieve/pii/S0034425711003543. 10.1016/j.rse.2011.10.006.
13. Ide R., Oguma H. A cost-effective monitoring method using digital time-lapse cameras for detecting temporal and spatial variations of snowmelt and vegetation phenology in alpine ecosystems. Ecol. Inform. 2013, 16:25-34. http://www.sciencedirect.com/science/article/pii/S1574954113000290. 10.1016/j.ecoinf.2013.04.003.
14. Jenkins J.P., Richardson A.D., Braswell B.H., Ollinger S.V., Hollinger D.Y., Smith M.L. Refining light-use efficiency calculations for a deciduous forest canopy using simultaneous tower-based carbon flux and radiometric measurements. Agric. Forest Meteorol. 2007, 143:64-79. http://www.sciencedirect.com/science/article/pii/S0168192306003613. 10.1016/j.agrformet.2006.11.008.
15. Julitta T., Cremonese E., Migliavacca M., Colombo R., Galvagno M., Siniscalco C., Rossini M., Fava F., Cogliati S., di Cella U.M., Menzel A. Using digital camera images to analyse snowmelt and phenology of a subalpine grassland. Agric. Forest Meteorol. 2014, 198-199:116-125. http://www.sciencedirect.com/science/article/pii/S0168192314001981. 10.1016/j.agrformet.2014.08.007.
16. Keenan T.F., Darby B., Felts E., Sonnentag O., Friedl M., Hufkens K., O' Keefe J.F., Klosterman S., Munger J.W., Toomey M., Richardson A.D. Tracking forest phenology and seasonal physiology using digital repeat photography: a critical assessment. Ecol. Appl. 2014, 140206175103002. http://www.esajournals.org/doi/abs/10.1890/13-0652.1. 10.1890/13-0652.1.
17. Kline M. Calculus: An Intuitive and Physical Approach (Second Edition) (Google eBook) 1998, Dover Publications, http://books.google.com/books?id=tZy8AQAAQBAJ&pgis=1.
18. Klosterman S.T., Hufkens K., Gray J.M., Melaas E., Sonnentag O., Lavine I., Mitchell L., Norman R., Friedl M.A., Richardson A.D. Evaluating remote sensing of deciduous forest phenology at multiple spatial scales using PhenoCam imagery. Biogeosciences 2014, 11:4305-4320.
19. Lechowicz M.J. Why do temperate deciduous trees leaf out at different times? Adaptation and ecology of forest communities. Am. Nat. 1984, 124:821-842. http://www.jstor.org/stable/2461303.
20. Migliavacca M., Cremonese E., Colombo R., Busetto L., Galvagno M., Ganis L., Meroni M., Pari E., Rossini M., Siniscalco C., Morra di Cella U. European larch phenology in the Alps: can we grasp the role of ecological factors by combining field observations and inverse modelling?. Int. J. Biometeorol. 2008, 52:587-605. http://www.ncbi.nlm.nih.gov/pubmed/18437430. 10.1007/s00484-008-0152-9.
21. 2 uptake. Agric. Forest Meteorol. 2011, 151:1325-1337.
22. Mizunuma T., Wilkinson M., Eaton L., Mencuccini E.M., Morison I.L., Grace J.J. The relationship between carbon dioxide uptake and canopy colour from two camera systems in a deciduous forest in southern England. Funct. Ecol. 2013, 27:196-207. http://doi.wiley.com/10.1111/1365-2435.12026. 10.1111/1365-2435.12026.
23. Nasahara K., Nagai S. Review: Development of an in-situ observation network for terrestrial ecological remote sensing - the phenological eyes network (pen). Ecol. Res. 2015, 30:211-223. 10.1007/s11284-014-1239-x.
24. Papale D., Reichstein M., Aubinet M., Canfora E., Bernhofer C., Kutsch W., Longdoz B., Rambal S., Valentini R., Vesala T., Yakir D. Towards a standardized processing of Net Ecosystem Exchange measured with eddy covariance technique: algorithms and uncertainty estimation. Biogeosciences 2006, 3:571-583.
25. Petach A.R., Toomey M., Aubrecht D.M., Richardson A.D. Monitoring vegetation phenology using an infrared-enabled security camera. Agric. Forest Meteorol. 2014, 195-196:143-151. http://linkinghub.elsevier.com/retrieve/pii/S0168192314001257. 10.1016/j.agrformet.2014.05.008.
26. R Core Team R. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing 2015, Austria, Vienna, http://www.R-project.org/.
27. Richardson A., Jenkins J., Braswell B., Hollinger D., Ollinger S., Smith M.L. Use of digital webcam images to track spring green-up in a deciduous broadleaf forest. Oecologia 2007, 152:323-334. 10.1007/s00442-006-0657-z.
28. Richardson A.D., Bailey A.S., Denny E.G., Martin C.W., O'Keefe J. Phenology of a northern hardwood forest canopy. Glob. Change Biol. 2006, 12:1174-1188.
29. Richardson A.D., Braswell B.H., Hollinger D.Y., Jenkins J.P., Ollinger S.V. Near-surface remote sensing of spatial and temporal variation in canopy phenology. Ecol. Appl. 2009, 19:1417-1428.
30. Richardson A.D., Keenan T.F., Migliavacca M., Ryu Y., Sonnentag O., Toomey M. Climate change, phenology, and phenological control of vegetation feedbacks to the climate system. Agric. Forest Meteorol. 2013, 169:156-173.
31. Sonnentag O., Hufkens K., Teshera-Sterne C., Young A.M., Friedl M., Braswell B.H., Milliman T., O'Keefe J., Richardson A.D. Digital repeat photography for phenological research in forest ecosystems. Agric. Forest Meteorol. 2012, 152:159-177.
32. Soudani K., Hmimina G., Delpierre N., Pontailler J.Y., Aubinet M., Bonal D., Caquet B., de Grandcourt A., Burban B., Flechard C., Guyon D., Granier A., Gross P., Heinesh B., Longdoz B., Loustau D., Moureaux C., Ourcival J.M., Rambal S., Saint André L., Dufrêne E. Ground-based Network of NDVI measurements for tracking temporal dynamics of canopy structure and vegetation phenology in different biomes. Remote Sens. Environ. 2012, 123:234-245. 10.1016/j.rse.2012.03.012.
33. White M.A., Nemani R.R. Real-time monitoring and short-term forecasting of land surface phenology. Remote Sens. Environ. 2006, 104:43-49. http://www.sciencedirect.com/science/article/pii/S0034425706001660. 10.1016/j.rse.2006.04.014.
34. Wingate L., Ogée J., Cremonese E., Filippa G., Mizunuma T., Migliavacca M., Moisy C., Wilkinson M., Moureaux C., Wohlfahrt G., Hammerle A., Hörtnagl L., Gimeno C., Porcar-Castell A., Galvagno M., Nakaji T., Morison J., Kolle O., Knohl A., Kutsch W., Kolari P., Nikinmaa E., Ibrom A., Gielen B., Eugster W., Balzarolo M., Papale D., Klumpp K., Köstner B., Grünwald T., Joffre R. Interpreting canopy development and physiology using the EUROPhen camera network at flux sites. Biogeosci. Discuss. 2015, 12:7979-8034. http://www.biogeosciences-discuss.net/12/7979/2015/. 10.5194/bgd-12-7979-2015.
35. Woebbecke D., Meyer G., Von Bargen K., Mortensen D. Color indices for weed identification under various soil, residue, and lighting conditions. Trans. ASAE 1995, 38:259-269. http://cat.inist.fr/?aModele=afficheN&cpsidt=3503524.
36. Zhang X., Friedl M., Schaaf a., Strahler C.B., Hodges A.H., Gao J.C.F., Reed F., Huete B.C.A. Monitoring vegetation phenology using MODIS. Remote Sens. Environ. 2003, 84:471-475. doi: 10.1016/S0034-4257(02)00135-9.