Remote phenology: Applying machine learning to detect phenological patterns in a cerrado savanna

Plant phenology has gained importance in the context of global change research, stimulating the development of new technologies for phenological observation. Digital cameras have been successfully used as multi-channel imaging sensors, providing measures of leaf color change information (RGB channels), or leafing phenological changes in plants. We monitored leaf-changing patterns of a cerrado-savanna vegetation by taken daily digital images. We extract RGB channels from digital images and correlated with phenological changes. Our first goals were: (1) to test if the color change information is able to characterize the phenological pattern of a group of species; and (2) to test if individuals from the same functional group may be automatically identified using digital images. In this paper, we present a machine learning approach to detect phenological patterns in the digital images. Our preliminary results indicate that: (1) extreme hours (morning and afternoon) are the best for identifying plant species; and (2) different plant species present a different behavior with respect to the color change information. Based on those results, we suggest that individuals from the same functional group might be identified using digital images, and introduce a new tool to help phenology experts in the species identification and location on-the-ground. ©2012 IEEE.

Applying machine learning based on multiscale classifiers to detect remote phenology patterns in Cerrado savanna trees

Plant phenology is one of the most reliable indicators of species responses to global climate change, motivating the development of new technologies for phenological monitoring. Digital cameras or near remote systems have been efficiently applied as multi-channel imaging sensors, where leaf color information is extracted from the RGB (Red, Green, and Blue) color channels, and the changes in green levels are used to infer leafing patterns of plant species. In this scenario, texture information is a great ally for image analysis that has been little used in phenology studies. We monitored leaf-changing patterns of Cerrado savanna vegetation by taking daily digital images. We extract RGB channels from the digital images and correlate them with phenological changes. Additionally, we benefit from the inclusion of textural metrics for quantifying spatial heterogeneity. Our first goals are: (1) to test if color change information is able to characterize the phenological pattern of a group of species; (2) to test if the temporal variation in image texture is useful to distinguish plant species; and (3) to test if individuals from the same species may be automatically identified using digital images. In this paper, we present a machine learning approach based on multiscale classifiers to detect phenological patterns in the digital images. Our results indicate that: (1) extreme hours (morning and afternoon) are the best for identifying plant species; (2) different plant species present a different behavior with respect to the color change information; and (3) texture variation along temporal images is promising information for capturing phenological patterns. Based on those results, we suggest that individuals from the same species and functional group might be identified using digital images, and introduce a new tool to help phenology experts in the identification of new individuals from the same species in the image and their location on the ground. © 2013 Elsevier B.V. All rights reserved.

Deriving vegetation indices for phenology analysis using genetic programming

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

The phenology of phytoplankton blooms: ecosystems indicators from remote sensing

Remote sensing offers many advantages in the development of ecosystem indicators for the pelagic zone of the ocean. Particularly suitable in this context are the indicators arising from time series that can be constructed from remotely sensed data. For example, using ocean-colour radiometry, the phenology of phytoplankton blooms can be assessed. Metrics defined in this way show promise as informative indicators for the entire pelagic ecosystem. A simple phytoplankton–substrate model, with forcing dependent on latitude and day number is used to explore the qualitative features of bloom phenology for comparison with the results observed in a suite of 10-year time series of chlorophyll concentration, as assessed by remote sensing, from the Northwest Atlantic Ocean. The model reveals features of the dynamics that might otherwise have been overlooked in evaluation of the observational data.

Phytoplankton phenology indices in coral reef ecosystems: Application to ocean-color observations in the Red Sea

Phytoplankton, at the base of the marine food web, represent a fundamental food source in coral reef ecosystems. The timing (phenology) and magnitude of the phytoplankton biomass are major determinants of trophic interactions. The Red Sea is one of the warmest and most saline basins in the world, characterized by an arid tropical climate regulated by the monsoon. These extreme conditions are particularly challenging for marine life. Phytoplankton phenological indices provide objective and quantitative metrics to characterize phytoplank- ton seasonality. The indices i.e. timings of initiation, peak, termination and duration are estimated here using 15 years (1997–2012) of remote sensing ocean-color data from the European Space Agency (ESA) Climate Change Initiative project (OC-CCI) in the entire Red Sea basin. The OC-CCI product, comprising merged and bias-corrected observations from three independent ocean-color sensors (SeaWiFS, MODIS and MERIS), and processed using the POLYMER algorithm (MERIS period), shows a significant increase in chlorophyll data cover- age, especially in the southern Red Sea during the months of summer NW monsoon. In open and reef-bound coastal waters, the performance of OC-CCI chlorophyll data is shown to be comparable with the performance of other standard chlorophyll products for the global oceans. These features have permitted us to investigate phytoplankton phenology in the entire Red Sea basin, and during both winter SE monsoon and summer NW monsoon periods. The phenological indices are estimated in the four open water provinces of the basin, and further examined at six coral reef complexes of particular socio-economic importance in the Red Sea, including Siyal Islands, Sharm El Sheikh, Al Wajh bank, Thuwal reefs, Al Lith reefs and Farasan Islands. Most of the open and deeper waters of the basin show an apparent higher chlorophyll concentration and longer duration of phyto- plankton growth during the winter period (relative to the summer phytoplankton growth period). In contrast, most of the reef-bound coastal waters display equal or higher peak chlorophyll concentrations and equal or lon- ger duration of phytoplankton growth during the summer period (relative to the winter phytoplankton growth period). The ecological and biological significance of the phytoplankton seasonal characteristics are discussed in context of ecosystem state assessment, and particularly to support further understanding of the structure and functioning of coral reef ecosystems in the Red Sea.

European plant phenology and climate as seen in a 20-year AVHRR land-surface parameter dataset

Vegetation distribution and state have been measured since 1981 by the AVHRR (Advanced Very High Resolution Radiometer) instrument through satellite remote sensing. In this study a correction method is applied to the Pathfinder NDVI (Normalized Difference Vegetation Index) data to create a continuous European vegetation phenology dataset of a 10-day temporal and 0.1° spatial resolution; additionally, land surface parameters for use in biosphere–atmosphere modelling are derived. The analysis of time-series from this dataset reveals, for the years 1982–2001, strong seasonal and interannual variability in European land surface vegetation state. Phenological metrics indicate a late and short growing season for the years 1985–1987, in addition to early and prolonged activity in the years 1989, 1990, 1994 and 1995. These variations are in close agreement with findings from phenological measurements at the surface; spring phenology is also shown to correlate particularly well with anomalies in winter temperature and winter North Atlantic Oscillation (NAO) index. Nevertheless, phenological metrics, which display considerable regional differences, could only be determined for vegetation with a seasonal behaviour. Trends in the phenological phases reveal a general shift to earlier (−0.54 days year−1) and prolonged (0.96 days year−1) growing periods which are statistically significant, especially for central Europe.

Lake ice phenology from AVHRR data for European lakes: An automated two-step extraction method

Several lake ice phenology studies from satellite data have been undertaken. However, the availability of long-term lake freeze-thaw-cycles, required to understand this proxy for climate variability and change, is scarce for European lakes. Long time series from space observations are limited to few satellite sensors. Data of the Advanced Very High Resolution Radiometer (AVHRR) are used in account of their unique potential as they offer each day global coverage from the early 1980s expectedly until 2022. An automatic two-step extraction was developed, which makes use of near-infrared reflectance values and thermal infrared derived lake surface water temperatures to extract lake ice phenology dates. In contrast to other studies utilizing thermal infrared, the thresholds are derived from the data itself, making it unnecessary to define arbitrary or lake specific thresholds. Two lakes in the Baltic region and a steppe lake on the Austrian–Hungarian border were selected. The later one was used to test the applicability of the approach to another climatic region for the time period 1990 to 2012. A comparison of the extracted event dates with in situ data provided good agreements of about 10 d mean absolute error. The two-step extraction was found to be applicable for European lakes in different climate regions and could fill existing data gaps in future applications. The extension of the time series to the full AVHRR record length (early 1980 until today) with adequate length for trend estimations would be of interest to assess climate variability and change. Furthermore, the two-step extraction itself is not sensor-specific and could be applied to other sensors with equivalent near- and thermal infrared spectral bands.

Comparison of fractal dimensions based on segmented NDVI fields obtained from different remote sensors.

Satellite image data have become an important source of information for monitoring vegetation and mapping land cover at several scales. Beside this, the distribution and phenology of vegetation is largely associated with climate, terrain characteristics and human activity. Various vegetation indices have been developed for qualitative and quantitative assessment of vegetation using remote spectral measurements. In particular, sensors with spectral bands in the red (RED) and near-infrared (NIR) lend themselves well to vegetation monitoring and based on them [(NIR - RED) / (NIR + RED)] Normalized Difference Vegetation Index (NDVI) has been widespread used. Given that the characteristics of spectral bands in RED and NIR vary distinctly from sensor to sensor, NDVI values based on data from different instruments will not be directly comparable. The spatial resolution also varies significantly between sensors, as well as within a given scene in the case of wide-angle and oblique sensors. As a result, NDVI values will vary according to combinations of the heterogeneity and scale of terrestrial surfaces and pixel footprint sizes. Therefore, the question arises as to the impact of differences in spectral and spatial resolutions on vegetation indices like the NDVI. The aim of this study is to establish a comparison between two different sensors in their NDVI values at different spatial resolutions.

Comparison of NDVI fields obtained from different remote sensors

Satellite image data have become an important source of information for monitoring vegetation and mapping land cover at several scales. Beside this, the distribution and phenology of vegetation is largely associated with climate, terrain characteristics and human activity. Various vegetation indices have been developed for qualitative and quantitative assessment of vegetation using remote spectral measurements. In particular, sensors with spectral bands in the red (RED) and near-infrared (NIR) lend themselves well to vegetation monitoring and based on them [(NIR - RED) / (NIR + RED)] Normalized Difference Vegetation Index (NDVI) has been widespread used. Given that the characteristics of spectral bands in RED and NIR vary distinctly from sensor to sensor, NDVI values based on data from different instruments will not be directly comparable. The spatial resolution also varies significantly between sensors, as well as within a given scene in the case of wide-angle and oblique sensors. As a result, NDVI values will vary according to combinations of the heterogeneity and scale of terrestrial surfaces and pixel footprint sizes. Therefore, the question arises as to the impact of differences in spectral and spatial resolutions on vegetation indices like the NDVI and their interpretation as a drought index. During 2012 three locations (at Salamanca, Granada and Córdoba) were selected and a periodic pasture monitoring and botanic composition were achieved. Daily precipitation, temperature and monthly soil water content were measurement as well as fresh and dry pasture weight. At the same time, remote sensing images were capture by DEIMOS-1 and MODIS of the chosen places. DEIMOS-1 is based on the concept Microsat-100 from Surrey. It is conceived for obtaining Earth images with a good enough resolution to study the terrestrial vegetation cover (20x20 m), although with a great range of visual field (600 km) in order to obtain those images with high temporal resolution and at a reduced cost. By contranst, MODIS images present a much lower spatial resolution (500x500 m). The aim of this study is to establish a comparison between two different sensors in their NDVI values at different spatial resolutions. Acknowledgements. This work was partially supported by ENESA under project P10 0220C-823. Funding provided by Spanish Ministerio de Ciencia e Innovación (MICINN) through project no. MTM2009-14621 and i-MATH No. CSD2006-00032 is greatly appreciated.

Polarimetric Response of Rice Fields at C-Band: Analysis and Phenology Retrieval

A set of ten RADARSAT-2 images acquired in fully polarimetric mode over a test site with rice fields in Seville, Spain, has been analyzed to extract the main features of the C-band radar backscatter as a function of rice phenology. After observing the evolutions versus phenology of different polarimetric observables and explaining their behavior in terms of scattering mechanisms present in the scene, a simple retrieval approach has been proposed. This algorithm is based on three polarimetric observables and provides estimates from a set of four relevant intervals of phenological stages. The validation against ground data, carried out at parcel level for a set of six stands and up to nine dates per stand, provides a 96% rate of coincidence. Moreover, an equivalent compact-pol retrieval algorithm has been also proposed and validated, providing the same performance at parcel level. In all cases, the inversion is carried out by exploiting a single satellite acquisition, without any other auxiliary information.

Crop Phenology Estimation Using a Multitemporal Model and a Kalman Filtering Strategy

In this letter, a new approach for crop phenology estimation with remote sensing is presented. The proposed methodology is aimed to exploit tools from a dynamical system context. From a temporal sequence of images, a geometrical model is derived, which allows us to translate this temporal domain into the estimation problem. The evolution model in state space is obtained through dimensional reduction by a principal component analysis, defining the state variables, of the observations. Then, estimation is achieved by combining the generated model with actual samples in an optimal way using a Kalman filter. As a proof of concept, an example with results obtained with this approach over rice fields by exploiting stacks of TerraSAR-X dual polarization images is shown.

Remote Sensing of Vegetation Change Across a Latitudinal Gradient in the Canadian Arctic

Global air surface temperatures and precipitation have increased over the last several decades resulting in a trend of greening across the Circumpolar Arctic. The spatial variability of warming and the inherent effects on plant communities has not proven to be uniform or homogeneous on global or local scales. We can apply remote sensing vegetation indices such as the Normalized Difference Vegetation Index (NDVI) to map and monitor vegetation change (e.g., phenology, greening, percent cover, and biomass) over time. It is important to document how Arctic vegetation is changing, as it will have large implications related to global carbon and surface energy budgets. The research reported here examined vegetation greening across different spatial and temporal scales at two disparate Arctic sites: Apex River Watershed (ARW), Baffin Island, and Cape Bounty Arctic Watershed Observatory (CBAWO), Melville Island, NU. To characterize the vegetation in the ARW, high spatial resolution WorldView-2 data were processed to create a supervised land-cover classification and model percent vegetation cover (PVC) (a similar process had been completed in a previous study for the CBAWO). Meanwhile, NDVI data spanning the past 30 years were derived from intermediate resolution Landsat data at the two Arctic sites. The land-cover classifications at both sites were used to examine the Landsat NDVI time series by vegetation class. Climate variables (i.e., temperature, precipitation and growing season length (GSL) were examined to explore the potential relationships of NDVI to climate warming. PVC was successfully modeled using high resolution data in the ARW. PVC and plant communities appear to reside along a moisture and altitudinal gradient. The NDVI time series demonstrated an overall significant increase in greening at the CBAWO (High Arctic site), specifically in the dry and mesic vegetation type. However, similar overall greening was not observed for the ARW (Low Arctic site). The overall increase in NDVI at the CBAWO was attributed to a significant increase in July temperatures, precipitation and GSL.

Seasonal mean air temperatures and ice phenology characteristics of Great Bear Lake and Great Slave Lake (2002-2009)

Time series of brightness temperatures (T(B)) from the Advanced Microwave Scanning Radiometer-Earth Observing System (AMSR-E) are examined to determine ice phenology variables on the two largest lakes of northern Canada: Great Bear Lake (GBL) and Great Slave Lake (GSL). T(B) measurements from the 18.7, 23.8, 36.5, and 89.0 GHz channels (H- and V- polarization) are compared to assess their potential for detecting freeze-onset/melt-onset and ice-on/ice-off dates on both lakes. The 18.7 GHz (H-pol) channel is found to be the most suitable for estimating these ice dates as well as the duration of the ice cover and ice-free seasons. A new algorithm is proposed using this channel and applied to map all ice phenology variables on GBL and GSL over seven ice seasons (2002-2009). Analysis of the spatio-temporal patterns of each variable at the pixel level reveals that: (1) both freeze-onset and ice-on dates occur on average about one week earlier on GBL than on GSL (Day of Year (DY) 318 and 333 for GBL; DY 328 and 343 for GSL); (2) the freeze-up process or freeze duration (freeze-onset to ice-on) takes a slightly longer amount of time on GBL than on GSL (about 1 week on average); (3) melt-onset and ice-off dates occur on average one week and approximately four weeks later, respectively, on GBL (DY 143 and 183 for GBL; DY 135 and 157 for GSL); (4) the break-up process or melt duration (melt-onset to ice-off) lasts on average about three weeks longer on GBL; and (5) ice cover duration estimated from each individual pixel is on average about three weeks longer on GBL compared to its more southern counterpart, GSL. A comparison of dates for several ice phenology variables derived from other satellite remote sensing products (e.g. NOAA Interactive Multisensor Snow and Ice Mapping System (IMS), QuikSCAT, and Canadian Ice Service Database) show that, despite its relatively coarse spatial resolution, AMSR-E 18.7 GHz provides a viable means for monitoring of ice phenology on large northern lakes.