e-pheno Monitoring plant phenology in the Western Alps Gianluca Filippa (and the e-pheno team) Aosta Valley Environmental Protection Agency ARPA VdA
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1 e-pheno Monitoring plant phenology in the Western Alps Gianluca Filippa (and the e-pheno team) Aosta Valley Environmental Protection Agency ARPA VdA Ceresole Reale 10 September ALPARC workshop
2 Why Phenology? e-pheno Project The Network Concluding remarks 1 Why Phenology? 2 e-pheno Project Overview 3 The Network PhenoNetwork NDVI database Webcam package 4 Concluding remarks
3 Why Phenology? e-pheno Project The Network Concluding remarks Phenology The rhythm of the seasons (Morisette et al 2009, Front. Ecol. Env.) It responds relatively fast to weather and climate changes It is easy to measure The study of phenology has a long tradition Phenology is the simplest process in which to track changes in the ecology of species in response to climate change (IPCC, 2007) In mountain ecosystems, phenology matters even more
4 Why Phenology? e-pheno Project The Network Concluding remarks Phenology in mountains Leaf emergence in Larch in Aosta Valley can vary by some 90 days in a single year Elevation, Continentality, Aspect, Precipitation, etc.
5 Why Phenology? e-pheno Project The Network Concluding remarks Phenology and Climate Change Spring onset is occurring earlier (Jeong et al 2011, Glob. Ch. Biol.)
6 Why Phenology? e-pheno Project The Network Concluding remarks Phenology and Climate Change Fall onset is occurring later (Jeong et al 2011, Glob. Ch. Biol.)
7 Why Phenology? e-pheno Project The Network Concluding remarks Phenology and Climate Change Growing seasons are becoming longer (Jeong et al 2011, Glob. Ch. Biol.)
8 Why Phenology? e-pheno Project The Network Concluding remarks Shifts in Phenology are clear! Most recent studies clearly demonstrated that plant phenology is shifting, and such shifts are very unlikely due to natural variability/fluctuation only. Hence, scientists agree on the existence of an anthropogenic component to climate change. Phenology is an useful tool to track the impact of climate change on natural ecosystems.
9 Why Phenology? e-pheno Project The Network Concluding remarks Phenology and its feedbacks Morisette et al 2009, Front. Ecol. Env. Weather and climate control phenology Phenology feedbacks on atmosphere and the climate system Shifts in phenology act on community structure, hence biodiversity
10 Why Phenology? e-pheno Project The Network Concluding remarks Keep an eye on Phenology But from how far? Field observer (precise, on single individuals, on single phases, expensive) Remote sensing (spatially integrated, poor spatial and time resolution, noisy signal) Near remote sensing (spatially integrated, high resolution, unmanned, cheap, need of some infrastructure)
11 Why Phenology? e-pheno Project The Network Concluding remarks Keep an eye on Phenology But from how far? Field observer (precise, on single individuals, on single phases, expensive) Remote sensing (spatially integrated, poor spatial and time resolution, noisy signal) Near remote sensing (spatially integrated, high resolution, unmanned, cheap, need of some infrastructure)
12 Why Phenology? e-pheno Project The Network Concluding remarks Keep an eye on Phenology But from how far? Field observer (precise, on single individuals, on single phases, expensive) Remote sensing (spatially integrated, poor spatial and time resolution, noisy signal) Near remote sensing (spatially integrated, high resolution, unmanned, cheap, need of some infrastructure)
13 Why Phenology? e-pheno Project The Network Concluding remarks Keep an eye on Phenology But from how far? Field observer (precise, on single individuals, on single phases, expensive) Remote sensing (spatially integrated, poor spatial and time resolution, noisy signal) Near remote sensing (spatially integrated, high resolution, unmanned, cheap, need of some infrastructure)
14 Why Phenology? e-pheno Project The Network Concluding remarks What do we measure? We decided to focus on two instruments: NDVI and Webcams. They consist of robust, simple sensors They are good indicators of the seasonal development of the vegetation cover We have (or are currently developing) the know-how to handle these data They are fairly inexpensive
15 Why Phenology? e-pheno Project The Network Concluding remarks NDVI: Rationale One or two bands sensors: NIR, R, G, B,... (Skye) Upward e downward sensors connected to datalogger Possibility to calculate different indices (eg NDVI = NIR R ), PRI,...) NIR+R NDVI seasonal trajectories can be associated to plant development and, thereby phenology.
16 Why Phenology? e-pheno Project The Network Concluding remarks Webcams: Rationale Torgnon Larch stand, 2100 m ASL
17 Why Phenology? e-pheno Project The Network Concluding remarks Webcams: seasonal trajectory From the red green and blue coordinates of a given number of pixels an Index of greenness is computed
18 Why Phenology? e-pheno Project The Network Concluding remarks Overview The project started in 2008 cooperation project Italy-France (Interreg Alcotra) PhenoAlp ( ) e-pheno ( ) Italy - Aosta Valley (ARPA, Parco Naturale Mont Avic, Parco Nazionale Gran Paradiso) France - (CREA, Parc National des Ecrins, LECA Grenoble, Parc des Bauges) field observations, sensor based observations (NDVI, webcam), schools engagement
19 Why Phenology? e-pheno Project The Network Concluding remarks Overview The project started in 2008 cooperation project Italy-France (Interreg Alcotra) PhenoAlp ( ) e-pheno ( ) Italy - Aosta Valley (ARPA, Parco Naturale Mont Avic, Parco Nazionale Gran Paradiso) France - (CREA, Parc National des Ecrins, LECA Grenoble, Parc des Bauges) field observations, sensor based observations (NDVI, webcam), schools engagement
20 Why Phenology? e-pheno Project The Network Concluding remarks Overview The project started in 2008 cooperation project Italy-France (Interreg Alcotra) PhenoAlp ( ) e-pheno ( ) Italy - Aosta Valley (ARPA, Parco Naturale Mont Avic, Parco Nazionale Gran Paradiso) France - (CREA, Parc National des Ecrins, LECA Grenoble, Parc des Bauges) field observations, sensor based observations (NDVI, webcam), schools engagement
21 Why Phenology? e-pheno Project The Network Concluding remarks PhenoNetwork NDVI database Webcam package North Western Alps phenological network Webcam sensors (10 sites: 5IT, 5FR)
22 Why Phenology? e-pheno Project The Network Concluding remarks PhenoNetwork NDVI database Webcam package North Western Alps phenological network Webcam sensors (10 sites: 5IT, 5FR) most sites installed in ecosystems: grasslands ( m asl) and subalpine (< 2000 m asl) larch forests common protocols and set-up but different cameras storing and processing strategy under discussion
23 Why Phenology? e-pheno Project The Network Concluding remarks PhenoNetwork NDVI database Webcam package North Western Alps phenological network Webcam sensors (10 sites: 5IT, 5FR) most sites installed in ecosystems: grasslands ( m asl) and subalpine (< 2000 m asl) larch forests common protocols and set-up but different cameras storing and processing strategy under discussion
24 Why Phenology? e-pheno Project The Network Concluding remarks PhenoNetwork NDVI database Webcam package North Western Alps phenological network Webcam sensors (10 sites: 5IT, 5FR) most sites installed in ecosystems: grasslands ( m asl) and subalpine (< 2000 m asl) larch forests common protocols and set-up but different cameras storing and processing strategy under discussion
25 Why Phenology? e-pheno Project The Network Concluding remarks PhenoNetwork NDVI database Webcam package North Western Alps phenological network Webcam sensors (10 sites: 5IT, 5FR) most sites installed in ecosystems: grasslands ( m asl) and subalpine (< 2000 m asl) larch forests common protocols and set-up but different cameras storing and processing strategy under discussion
26 Why Phenology? e-pheno Project The Network Concluding remarks PhenoNetwork NDVI database Webcam package North Western Alps phenological network Webcam sensors (10 sites: 5IT, 5FR) most sites installed in ecosystems: grasslands ( m asl) and subalpine (< 2000 m asl) larch forests common protocols and set-up but different cameras storing and processing strategy under discussion
27 Why Phenology? e-pheno Project The Network Concluding remarks PhenoNetwork NDVI database Webcam package NDVI database NDVI database (12 sites: 5IT, 7FR) but other 6 from LECA ready to be included
28 Why Phenology? e-pheno Project The Network Concluding remarks PhenoNetwork NDVI database Webcam package NDVI database NDVI database (12 sites: 5IT, 7FR) but other 6 from LECA ready to be included similar installation protocols but different sensors (Skye and ESE-LECA-Paris) most sites installed in ecosystems: grasslands ( m asl) and subalpine (< 2000 m asl) larch forests storing and processing strategy defined (e-pheno database)
29 Why Phenology? e-pheno Project The Network Concluding remarks PhenoNetwork NDVI database Webcam package NDVI database NDVI database (12 sites: 5IT, 7FR) but other 6 from LECA ready to be included similar installation protocols but different sensors (Skye and ESE-LECA-Paris) most sites installed in ecosystems: grasslands ( m asl) and subalpine (< 2000 m asl) larch forests storing and processing strategy defined (e-pheno database)
30 Why Phenology? e-pheno Project The Network Concluding remarks PhenoNetwork NDVI database Webcam package NDVI database NDVI database (12 sites: 5IT, 7FR) but other 6 from LECA ready to be included similar installation protocols but different sensors (Skye and ESE-LECA-Paris) most sites installed in ecosystems: grasslands ( m asl) and subalpine (< 2000 m asl) larch forests storing and processing strategy defined (e-pheno database)
31 Why Phenology? e-pheno Project The Network Concluding remarks PhenoNetwork NDVI database Webcam package NDVI database NDVI database (12 sites: 5IT, 7FR) but other 6 from LECA ready to be included similar installation protocols but different sensors (Skye and ESE-LECA-Paris) most sites installed in ecosystems: grasslands ( m asl) and subalpine (< 2000 m asl) larch forests storing and processing strategy defined (e-pheno database)
32 Why Phenology? e-pheno Project The Network Concluding remarks PhenoNetwork NDVI database Webcam package NDVI database NDVI database (12 sites: 5IT, 7FR) but other 6 from LECA ready to be included similar installation protocols but different sensors (Skye and ESE-LECA-Paris) most sites installed in ecosystems: grasslands ( m asl) and subalpine (< 2000 m asl) larch forests storing and processing strategy defined (e-pheno database)
33 Why Phenology? e-pheno Project The Network Concluding remarks PhenoNetwork NDVI database Webcam package NDVI database
34 Why Phenology? e-pheno Project The Network Concluding remarks PhenoNetwork NDVI database Webcam package NDVI sensors comparison
35 Why Phenology? e-pheno Project The Network Concluding remarks PhenoNetwork NDVI database Webcam package NDVI sensors comparison Torgnon Larch stand
36 Why Phenology? e-pheno Project The Network Concluding remarks PhenoNetwork NDVI database Webcam package NDVI sensors comparison Torgnon Larch stand
37 Why Phenology? e-pheno Project The Network Concluding remarks PhenoNetwork NDVI database Webcam package Image Processing package A package in the popular software for statistical computing R R Core Team (2013). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. Open source, cost free Highly flexible Available for download soon (1 month) at
38 Why Phenology? e-pheno Project The Network Concluding remarks PhenoNetwork NDVI database Webcam package ROI (Region of Interest) definition User can define ROIs on a reference image clicking on ROIs vertexes PNGP: Orvieille site
39 Why Phenology? e-pheno Project The Network Concluding remarks PhenoNetwork NDVI database Webcam package Data processing On each ROI for each date average RGB values are computed (but gridded analysis is under development) Greenees index (GI) is computed as G/(R+G+B) GI data is cleaned with a sequential filtering procedure (low quality images, bad light, rainy days) Seasonal trajectories are modelled by means of various equations (double logistic equations) Phenological thresholds are extracted with various methods (fixed (i.e. half peak) or based on inflection points of derivatives) Uncertainty is computed bootstrapping the residuals
40 Why Phenology? e-pheno Project The Network Concluding remarks PhenoNetwork NDVI database Webcam package Orvieille 2012: Different ROIs with different trajectories
41 Why Phenology? e-pheno Project The Network Concluding remarks PhenoNetwork NDVI database Webcam package Data processing On each ROI for each date average RGB values are computed (but gridded analysis is under development) Greenees index (GI) is computed as G/(R+G+B) GI data is cleaned with a sequential filtering procedure (low quality images, bad light, rainy days) Seasonal trajectories are modelled by means of various equations (double logistic equations) Phenological thresholds are extracted with various methods (fixed (i.e. half peak) or based on inflection points of derivatives) Uncertainty is computed bootstrapping the residuals
42 Why Phenology? e-pheno Project The Network Concluding remarks PhenoNetwork NDVI database Webcam package Torgnon Larch site: 2012
43 Why Phenology? e-pheno Project The Network Concluding remarks PhenoNetwork NDVI database Webcam package Data processing On each ROI for each date average RGB values are computed (but gridded analysis is under development) Greenees index (GI) is computed as G/(R+G+B) GI data is cleaned with a sequential filtering procedure (low quality images, bad light, rainy days) Seasonal trajectories are modelled by means of various equations (double logistic equations) Phenological thresholds are extracted with various methods (fixed (i.e. half peak) or based on inflection points of derivatives) Uncertainty is computed bootstrapping the residuals
44 Why Phenology? e-pheno Project The Network Concluding remarks PhenoNetwork NDVI database Webcam package Filtering procedure applied to Orvieille 2012 raw data
45 Why Phenology? e-pheno Project The Network Concluding remarks PhenoNetwork NDVI database Webcam package Data processing On each ROI for each date average RGB values are computed (but gridded analysis is under development) Greenees index (GI) is computed as G/(R+G+B) GI data is cleaned with a sequential filtering procedure (low quality images, bad light, rainy days) Seasonal trajectories are modeled by means of various equations (double logistic equations) Phenological thresholds are extracted with various methods (fixed (i.e. half peak) or based on inflection points of derivatives) Uncertainty is computed bootstrapping the residuals
46 Why Phenology? e-pheno Project The Network Concluding remarks PhenoNetwork NDVI database Webcam package The double logistic function and the extracted thresholds are as in Klosterman et al. 2014
47 Why Phenology? e-pheno Project The Network Concluding remarks PhenoNetwork NDVI database Webcam package The double logistic function is as in Klosterman et al. 2014, extracted thresholds are computed according to Gu et al. 2003
48 Why Phenology? e-pheno Project The Network Concluding remarks PhenoNetwork NDVI database Webcam package The package Developed in collaboration with PHENOCAM ( Highly flexible (5 fitting methods, 5 thresholding approaches) Tested on a large database (250 site-years) Covering a wide range of ecosystems (from arid to alpine grasslands, from deciduous tropical to coniferous boreal forests) Designed to be user-friendly
49 Why Phenology? e-pheno Project The Network Concluding remarks Costs NDVI measurement system The sensor itself (Skye) Power supply (solar panel + battery) Data logger Total: 3-3.5k Euro Webcam measurement system The webcam itself (Reflex Nikon) Power supply Data logger and case Total: 4-5k Euro Additional costs: biweekly/monthly visit to the site
50 Why Phenology? e-pheno Project The Network Concluding remarks Costs NDVI measurement system The sensor itself (Skye) Power supply (solar panel + battery) Data logger Total: 3-3.5k Euro Webcam measurement system The webcam itself (Reflex Nikon) Power supply Data logger and case Total: 4-5k Euro Additional costs: biweekly/monthly visit to the site
51 Why Phenology? e-pheno Project The Network Concluding remarks Costs NDVI measurement system The sensor itself (Skye) Power supply (solar panel + battery) Data logger Total: 3-3.5k Euro Webcam measurement system The webcam itself (Reflex Nikon) Power supply Data logger and case Total: 4-5k Euro Additional costs: biweekly/monthly visit to the site
52 Why Phenology? e-pheno Project The Network Concluding remarks Costs NDVI measurement system The sensor itself (Skye) Power supply (solar panel + battery) Data logger Total: 3-3.5k Euro Webcam measurement system The webcam itself (Reflex Nikon) Power supply Data logger and case Total: 4-5k Euro Additional costs: biweekly/monthly visit to the site
53 Why Phenology? e-pheno Project The Network Concluding remarks Summary The e-pheno project allowed to build/extend a network of NDVI and WEBCAM measurements in the North Western Alps A database was built to host NDVI data, and it is ready to include new sites A package software has been designed to process Webcam images Data, software and know-how are freely available, in an open-source perspective
54 Why Phenology? e-pheno Project The Network Concluding remarks Summary The e-pheno project allowed to build/extend a network of NDVI and WEBCAM measurements in the North Western Alps A database was built to host NDVI data, and it is ready to include new sites A package software has been designed to process Webcam images Data, software and know-how are freely available, in an open-source perspective
55 Why Phenology? e-pheno Project The Network Concluding remarks Summary The e-pheno project allowed to build/extend a network of NDVI and WEBCAM measurements in the North Western Alps A database was built to host NDVI data, and it is ready to include new sites A package software has been designed to process Webcam images Data, software and know-how are freely available, in an open-source perspective
56 Why Phenology? e-pheno Project The Network Concluding remarks Summary The e-pheno project allowed to build/extend a network of NDVI and WEBCAM measurements in the North Western Alps A database was built to host NDVI data, and it is ready to include new sites A package software has been designed to process Webcam images Data, software and know-how are freely available, in an open-source perspective
57 Why Phenology? e-pheno Project The Network Concluding remarks Summary The e-pheno project allowed to build/extend a network of NDVI and WEBCAM measurements in the North Western Alps A database was built to host NDVI data, and it is ready to include new sites A package software has been designed to process Webcam images Data, software and know-how are freely available, in an open-source perspective
58 Why Phenology? e-pheno Project The Network Concluding remarks Further steps Improve data intercomparison (different sensors, different set-up, etc.) Enlarge the network: incorporate existing sites, populate the database Enlarge the network: include new sites (e-pheno is finishing, but the network goes on! Parks are welcome) Increase range of ecosystem types, climate, i.e. increase the representativeness of observation network Provide know-how and installation instructions for new partners/sites More info
59 Why Phenology? e-pheno Project The Network Concluding remarks Further steps Improve data intercomparison (different sensors, different set-up, etc.) Enlarge the network: incorporate existing sites, populate the database Enlarge the network: include new sites (e-pheno is finishing, but the network goes on! Parks are welcome) Increase range of ecosystem types, climate, i.e. increase the representativeness of observation network Provide know-how and installation instructions for new partners/sites More info
60 Why Phenology? e-pheno Project The Network Concluding remarks Further steps Improve data intercomparison (different sensors, different set-up, etc.) Enlarge the network: incorporate existing sites, populate the database Enlarge the network: include new sites (e-pheno is finishing, but the network goes on! Parks are welcome) Increase range of ecosystem types, climate, i.e. increase the representativeness of observation network Provide know-how and installation instructions for new partners/sites More info
61 Why Phenology? e-pheno Project The Network Concluding remarks Further steps Improve data intercomparison (different sensors, different set-up, etc.) Enlarge the network: incorporate existing sites, populate the database Enlarge the network: include new sites (e-pheno is finishing, but the network goes on! Parks are welcome) Increase range of ecosystem types, climate, i.e. increase the representativeness of observation network Provide know-how and installation instructions for new partners/sites More info
62 Why Phenology? e-pheno Project The Network Concluding remarks Further steps Improve data intercomparison (different sensors, different set-up, etc.) Enlarge the network: incorporate existing sites, populate the database Enlarge the network: include new sites (e-pheno is finishing, but the network goes on! Parks are welcome) Increase range of ecosystem types, climate, i.e. increase the representativeness of observation network Provide know-how and installation instructions for new partners/sites More info
63 Why Phenology? e-pheno Project The Network Concluding remarks Further steps Improve data intercomparison (different sensors, different set-up, etc.) Enlarge the network: incorporate existing sites, populate the database Enlarge the network: include new sites (e-pheno is finishing, but the network goes on! Parks are welcome) Increase range of ecosystem types, climate, i.e. increase the representativeness of observation network Provide know-how and installation instructions for new partners/sites More info
64 Why Phenology? e-pheno Project The Network Concluding remarks Thanks for your attention Questions?
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