Global data for ecology and epidemiology: a novel algorithm for temporal Fourier processing MODIS data

Background. Remotely-sensed environmental data from earth-orbiting satellites are increasingly used to model the distribution and abundance of both plant and animal species, especially those of economic or conservation importance. Time series of data from the MODerate-resolution Imaging Spectroradiometer (MODIS) sensors on-board NASA's Terra and Aqua satellites offer the potential to capture environmental thermal and vegetation seasonality, through temporal Fourier analysis, more accurately than was previously possible using the NOAA Advanced Very High Resolution Radiometer (AVHRR) sensor data. MODIS data are composited over 8- or 16-day time intervals that pose unique problems for temporal Fourier analysis. Applying standard techniques to MODIS data can introduce errors of up to 30% in the estimation of the amplitudes and phases of the Fourier harmonics. Methodology/Principal Findings. We present a novel spline-based algorithm that overcomes the processing problems of composited MODIS data. The algorithm is tested on artificial data generated using randomly selected values of both amplitudes and phases, and provides an accurate estimate of the input variables under all conditions. The algorithm was then applied to produce layers that capture the seasonality in MODIS data for the period from 2001 to 2005. Conclusions/Significance. Global temporal Fourier processed images of 1 km MODIS data for Middle Infrared Reflectance, day- and night-time Land Surface Temperature (LST), Normalised Difference Vegetation Index (NDVI), and Enhanced Vegetation Index (EVI) are presented for ecological and epidemiological applications. The finer spatial and temporal resolution, combined with the greater geolocational and spectral accuracy of the MODIS instruments, compared with previous multi-temporal data sets, mean that these data may be used with greater confidence in species' distribution modelling

Classification of Satellite Time Series-derived Land Surface Phenology Focused on the Northern Fertile Crescent

Land surface phenology describes events in a seasonal vegetation cycle and can be used in a variety of applications from predicting onset of future drought conditions, to revealing potential limits of historical dry farming, to guiding more accurate dating of archeological sites. Traditional methods of monitoring vegetation phenology use data collected in situ. However, vegetation health indices derived from satellite remote sensor data, such as the normalized difference vegetation index (NDVI), have been used as proxy for vegetation phenology due to their repeated acquisition and broad area coverage. Land surface phenology is accessible in the NDVI satellite record when images are processed to be intercomparable over time and temporally ordered to create a time series. This study utilized NDVI time series to classify areas of similar vegetation phenology in the northern Fertile Crescent, an area from the middle Mediterranean coast to southern/south-eastern Turkey to western Iran and northern Iraq. Phenological monitoring of the northern Fertile Crescent is critical due to the area\u27s minimal water resources, susceptibility to drought, and understanding ancient historical reliance on precipitation for subsistence dry farming. Delineation of phenological classes provides areal and temporal synopsis of vegetation productivity time series. Phenological classes were developed from NDVI time series calculated from NOAA\u27s Advanced Very High Resolution Radiometer (AVHRR) imagery with 8 × 8 km spatial resolution over twenty-five years, and by NASA\u27s Moderate Resolution Imaging Spectroradiometer (MODIS) with 250 × 250 m spatial resolution over twelve years. Both AVHRR and MODIS time series were subjected to data reduction techniques in spatial and temporal dimensions. Optimized ISODATA clusters were developed for both of these data reduction techniques in order to compare the effects of spatial versus temporal aggregation. Within the northern Fertile Crescent study area, the spatial reduction technique showed increased cluster cohesion over the temporal reduction method. The latter technique showed an increase in temporal smoothing over the spatial reduction technique. Each technique has advantages depending on the desired spatial or temporal granularity. Additional work is required to determine optimal scale size for the spatial data reduction technique

Burnt area mapping in insular Southeast Asia using medium resolution satellite imagery

Burnt area mapping in humid tropical insular Southeast Asia using medium resolution (250-500m) satellite imagery is characterized by persisting cloud cover, wide range of land cover types, vast amount of wetland areas and highly varying fire regimes. The objective of this study was to deepen understanding of three major aspects affecting the implementation and limits of medium resolution burnt area mapping in insular Southeast Asia: 1) fire-induced spectral changes, 2) most suitable multitemporal compositing methods and 3) burn scars patterns and size distribution. The results revealed a high variation in fire-induced spectral changes depending on the pre-fire greenness of burnt area. It was concluded that this variation needs to be taken into account in change detection based burnt area mapping algorithms in order to maximize the potential of medium resolution satellite data. Minimum near infrared (MODIS band 2, 0.86μm) compositing method was found to be the most suitable for burnt area mapping purposes using Moderate Resolution Imaging Spectroradiometer (MODIS) data. In general, medium resolution burnt area mapping was found to be usable in the wetlands of insular Southeast Asia, whereas in other areas the usability was seriously jeopardized by the small size of burn scars. The suitability of medium resolution data for burnt area mapping in wetlands is important since recently Southeast Asian wetlands have become a major point of interest in many fields of science due to yearly occurring wild fires that not only degrade these unique ecosystems but also create regional haze problem and release globally significant amounts of carbon into the atmosphere due to burning peat. Finally, super-resolution MODIS images were tested but the test failed to improve the detection of small scars. Therefore, super-resolution technique was not considered to be applicable to regional level burnt area mapping in insular Southeast Asia.Laaja valikoima erilaisia maankäyttöluokkia, pilvisyys ja kosteikkoalueiden suuri määrä luovat erityispiirteet paloalueiden kartoitukselle Kaakkois-Aasian saariston kostean troppisissa olosuhteissa keskiresoluutioisilla (250m-500m) satelliittikuva-aineistoilla. Tämän tutkimuksen tavoitteena oli syventää ymmärrystä keskiresoluutioisen paloaluekartoituksen toteutukseen ja rajoituksiin Kaakkois-Aasian saaristossa vaikuttavista tekijöistä. Tutkimuksen tulokset paljastivat suurta vaihtelua tulipalojen aiheuttamissa heijastussäteilyn muutoksissa riippuen palaneen alueen vehreydestä ennen tulipaloa. Johtopäätöksenä todettiin että keskiresoluutioisten satelliittikuvien koko potentiaalin hyödyntämiseksi paloalueiden kartoituksessa tämä vaihtelu tulisi ottaa huomioon paloalueiden havainnointialgoritmeissa jotka perustuvat heijastussäteilyn muutosten seurantaan. Tähän ajatukseen perustuvaa paloalueiden kartoitusta myös kokeiltiin aineistoilla jotka oli tutkimuksissa todettu parhaiten tarkoitukseen sopiviksi. Paloalueiden muoto- ja kokojakauman analyysiin sekä käytännön testeihin perustuen keskiresoluutioinen paloalueiden kartoitus todettiin käyttökelpoiseksi Kaakkois-Aasian saariston kosteikkoalueilla. Muilla alueilla sen sijaan paloalueiden pieni koko uhkasi vakavasti sen käyttökelpoisuutta. Keskiresoluutioisten satelliittikuva-aineistojen käyttökelpoisuus paloalueiden kartoitukseen kosteikkoalueilla on kuitenkin merkittävää sillä viime aikoina Kaakkois-Aasian kosteikkoalueet ovat monilla tieteenaloilla nousseet kiinnostuksen kohteeksi vuosittain esiintyvien tulipalojen takia. Vuosittaiset tulipalot eivät ainoastaan heikennä näitä ainutlaatuisia ekosysteemejä vaan lähinnä palavan turpeen johdosta myös aiheuttavat pahoja alueellisia savusumuongelmia ja vapauttavat maailmanlaajuisesti merkittäviä määriä hiilidioksidia ilmakehään. Tämän tutkimuksen tulokset osaltaan luovat pohjaa yhä tarkempien alueellisten paloalueiden kartoitusmenetelmien kehittämiselle. Näillä menetelmillä kerättävä tieto paloalueiden laajuudesta ja sijainneista antaa muiden alojen tutkijoille yhä paremmat mahdollisuudet arvioida Kaakkois-Aasian saariston kosteikkoalueiden tulipalojen paikallisia, alueellisia ja maailmanlaajuisia vaikutuksia

QUANTIFICATION OF ERROR IN AVHRR NDVI DATA

Several influential Earth system science studies in the last three decades were based on Normalized Difference Vegetation Index (NDVI) data from Advanced Very High Resolution Radiometer (AVHRR) series of instruments. Although AVHRR NDVI data are known to have significant uncertainties resulting from incomplete atmospheric correction, orbital drift, sensor degradation, etc., none of these studies account for them. This is primarily because of unavailability of comprehensive and location-specific quantitative uncertainty estimates. The first part of this dissertation investigated the extent of uncertainty due to inadequate atmospheric correction in the widely used AVHRR NDVI datasets. This was accomplished by comparison with atmospherically corrected AVHRR data at AErosol RObotic NETwork (AERONET) sunphotometer sites in 1999. Of the datasets included in this study, Long Term Data Record (LTDR) was found to have least errors (precision=0.02 to 0.037 for clear and average atmospheric conditions) followed by Pathfinder AVHRR Land (PAL) (precision=0.0606 to 0.0418), and Top of Atmosphere (TOA) (precision=0.0613 to 0.0684). ` Although the use of field data is the most direct type of validation and is used extensively by the remote sensing community, it results in a single uncertainty estimate and does not account for spatial heterogeneity and the impact of spatial and temporal aggregation. These shortcomings were addressed by using Moderate Resolution Imaging Spectrometer (MODIS) data to estimate uncertainty in AVHRR NDVI data. However, before AVHRR data could be compared with MODIS data, the nonstationarity introduced by inter-annual variations in AVHRR NDVI data due to orbital drift had to be removed. This was accomplished by using a Bidirectional Reflectance Distribution Function (BRDF) correction technique originally developed for MODIS data. The results from the evaluation of AVHRR data using MODIS showed that in many regions minimal spatial aggregation will improve the precision of AVHRR NDVI data significantly. However temporal aggregation improved the precision of the data to a limited extent only. The research presented in this dissertation indicated that the NDVI change of ~0.03 to ~0.08 NDVI units in 10 to 20 years, frequently reported in recent literature, can be significant in some cases. However, unless spatially explicit uncertainty metrics are quantified for the specific spatiotemporal aggregation schemes used by these studies, the significance of observed differences between sites and temporal trends in NDVI will remain unknown

Estimation of Burned Area in the Northeastern Siberian Boreal Forest from a Long-Term Data Record (LTDR) 1982–2015 Time Series

A Bayesian classifier mapped the Burned Area (BA) in the Northeastern Siberian boreal forest (70°N 120°E–60°N 170°E) from 1982 to 2015. The algorithm selected the 0.05° (~5 km) Long-Term Data Record (LTDR) version 3 and 4 data sets to generate 10-day BA composites. Landsat-TM scenes of the entire study site in 2002, 2010, and 2011 assessed the spatial accuracy of this LTDR-BA product, in comparison to Moderate-Resolution Imaging Spectroradiometer (MODIS) MCD45A1 and MCD64A1 BA products. The LTDR-BA algorithm proves a reliable source to quantify BA in this part of Siberia, where comprehensive BA remote sensing products since the 1980s are lacking. Once grouped by year and decade, this study explored the trends in fire activity. The LTDR-BA estimates contained a high interannual variability with a maximum of 2.42 million ha in 2002, an average of 0.78 million ha/year, and a standard deviation of 0.61 million ha. Going from 6.36 in the 1980s to 10.21 million ha BA in the 2010s, there was a positive linear BA trend of approximately 1.28 million ha/decade during these last four decades in the Northeastern Siberian boreal forest

High Performance Computing Applications in Remote Sensing Studies for Land Cover Dynamics

Global and regional land cover studies require the ability to apply complex models on selected subsets of large amounts of multi-sensor and multi-temporal data sets that have been derived from raw instrument measurements using widely accepted pre-processing algorithms. The computational and storage requirements of most such studies far exceed what is possible on a single workstation environment. We have been pursuing a new approach that couples scalable and open distributed heterogeneous hardware with the development of high performance software for processing, indexing, and organizing remotely sensed data. Hierarchical data management tools are used to ingest raw data, create metadata, and organize the archived data so as to automatically achieve computational load balancing among the available nodes and minimize I/O overheads. We illustrate our approach with four specific examples. The first is the development of the first fast operational scheme for the atmospheric correction of Landsat TM scenes, while the second example focuses on image segmentation using a novel hierarchical connected components algorithm. Retrieval of global BRDF (Bidirectional Reflectance Distribution Function) in the red and near infrared wavelengths using four years (1983 to 1986) of Pathfinder AVHRR Land (PAL) data set is the focus of our third example. The fourth example is the development of a hierarchical data organization scheme that allows on-demand processing and retrieval of regional and global AVHRR data sets. Our results show that substantial improvements in computational times can be achieved by using the high performance computing technology

The CACAO Method for Smoothing, Gap Filling, and Characterizing Seasonal Anomalies in Satellite Time Series

Consistent, continuous, and long time series of global biophysical variables derived from satellite data are required for global change research. A novel climatology fitting approach called CACAO (Consistent Adjustment of the Climatology to Actual Observations) is proposed to reduce noise and fill gaps in time series by scaling and shifting the seasonal climatological patterns to the actual observations. The shift and scale CACAO parameters adjusted for each season allow quantifying shifts in the timing of seasonal phenology and inter-annual variations in magnitude as compared to the average climatology. CACAO was assessed first over simulated daily Leaf Area Index (LAI) time series with varying fractions of missing data and noise. Then, performances were analyzed over actual satellite LAI products derived from AVHRR Long-Term Data Record for the 1981-2000 period over the BELMANIP2 globally representative sample of sites. Comparison with two widely used temporal filtering methods-the asymmetric Gaussian (AG) model and the Savitzky-Golay (SG) filter as implemented in TIMESAT-revealed that CACAO achieved better performances for smoothing AVHRR time series characterized by high level of noise and frequent missing observations. The resulting smoothed time series captures well the vegetation dynamics and shows no gaps as compared to the 50-60% of still missing data after AG or SG reconstructions. Results of simulation experiments as well as confrontation with actual AVHRR time series indicate that the proposed CACAO method is more robust to noise and missing data than AG and SG methods for phenology extraction

Use of EO-1 Hyperion Data for Inter-Sensor Calibration of Vegetation Indices

Numerous satellite sensor systems useful in terrestrial Earth observation and monitoring have recently been launched and their derived products are increasingly being used in regional and global vegetation studies. The increasing availability of multiple sensors offer much opportunity for vegetation studies aimed at understanding the terrestrial carbon cycle, climate change, and land cover conversions. Potential applications include improved multiresolution characterization of the surface (scaling); improved optical-geometric characterization of vegetation canopies; improved assessments of surface phenology and ecosystem seasonal dynamics; and improved maintenance of long-term, inter-annual, time series data records. The Landsat series of sensors represent one group of sensors that have produced a long-term, archived data set of the Earth s surface, at fine resolution and since 1972, capable of being processed into useful information for global change studies (Hall et al., 1991)

Extracting ecological and biophysical information from AVHRR optical data: An integrated algorithm based on inverse modeling

Satellite remote sensing provides the only means of directly observing the entire surface of the Earth at regular spatial and temporal intervals

REMOTE SENSING DATA ANALYSIS FOR ENVIRONMENTAL AND HUMANITARIAN PURPOSES. The automation of information extraction from free satellite data.

This work is aimed at investigating technical possibilities to provide information on environmental parameters that can be used for risk management. The World food Program (WFP) is the United Nations Agency which is involved in risk management for fighting hunger in least-developed and low-income countries, where victims of natural and manmade disasters, refugees, displaced people and the hungry poor suffer from severe food shortages. Risk management includes three different phases (pre-disaster, response and post disaster) to be managed through different activities and actions. Pre disaster activities are meant to develop and deliver risk assessment, establish prevention actions and prepare the operative structures for managing an eventual emergency or disaster. In response and post disaster phase actions planned in the pre-disaster phase are executed focusing on saving lives and secondly, on social economic recovery. In order to optimally manage its operations in the response and post disaster phases, WFP needs to know, in order to estimate the impact an event will have on future food security as soon as possible, the areas affected by the natural disaster, the number of affected people, and the effects that the event can cause to vegetation. For this, providing easy-to-consult thematic maps about the affected areas and population, with adequate spatial resolution, time frequency and regular updating can result determining. Satellite remote sensed data have increasingly been used in the last decades in order to provide updated information about land surface with an acceptable time frequency. Furthermore, satellite images can be managed by automatic procedures in order to extract synthetic information about the ground condition in a very short time and can be easily shared in the web. The work of thesis, focused on the analysis and processing of satellite data, was carried out in cooperation with the association ITHACA (Information Technology for Humanitarian Assistance, Cooperation and Action), a center of research which works in cooperation with the WFP in order to provide IT products and tools for the management of food emergencies caused by natural disasters. These products should be able to facilitate the forecasting of the effects of catastrophic events, the estimation of the extension and location of the areas hit by the event, of the affected population and thereby the planning of interventions on the area that could be affected by food insecurity. The requested features of the instruments are: • Regular updating • Spatial resolution suitable for a synoptic analysis • Low cost • Easy consultation Ithaca is developing different activities to provide georeferenced thematic data to WFP users, such a spatial data infrastructure for storing, querying and manipulating large amounts of global geographic information, and for sharing it between a large and differentiated community; a system of early warning for floods, a drought monitoring tool, procedures for rapid mapping in the response phase in a case of natural disaster, web GIS tools to distribute and share georeferenced information, that can be consulted only by means of a web browser. The work of thesis is aimed at providing applications for the automatic production of base georeferenced thematic data, by using free global satellite data, which have characteristics suitable for analysis at a regional scale. In particular the main themes of the applications are water bodies and vegetation phenology. The first application aims at providing procedures for the automatic extraction of water bodies and will lead to the creation and update of an historical archive, which can be analyzed in order to catch the seasonality of water bodies and delineate scenarios of historical flooded areas. The automatic extraction of phenological parameters from satellite data will allow to integrate the existing drought monitoring system with information on vegetation seasonality and to provide further information for the evaluation of food insecurity in the post disaster phase. In the thesis are described the activities carried on for the development of procedures for the automatic processing of free satellite data in order to produce customized layers according to the exigencies in format and distribution of the final users. The main activities, which focused on the development of an automated procedure for the extraction of flooded areas, include the research of an algorithm for the classification of water bodies from satellite data, an important theme in the field of management of the emergencies due to flood events. Two main technologies are generally used: active sensors (radar) and passive sensors (optical data). Advantages for active sensors include the ability to obtain measurements anytime, regardless of the time of day or season, while passive sensors can only be used in the daytime cloud free conditions. Even if with radar technologies is possible to get information on the ground in all weather conditions, it is not possible to use radar data to obtain a continuous archive of flooded areas, because of the lack of a predetermined frequency in the acquisition of the images. For this reason the choice of the dataset went in favor of MODIS (Moderate Resolution Imaging Spectroradiometer), optical data with a daily frequency, a spatial resolution of 250 meters and an historical archive of 10 years. The presence of cloud coverage prevents from the acquisition of the earth surface, and the shadows due to clouds can be wrongly classified as water bodies because of the spectral response very similar to the one of water. After an analysis of the state of the art of the algorithms of automated classification of water bodies in images derived from optical sensors, the author developed an algorithm that allows to classify the data of reflectivity and to temporally composite them in order to obtain flooded areas scenarios for each event. This procedure was tested in the Bangladesh areas, providing encouraging classification accuracies. For the vegetation theme, the main activities performed, here described, include the review of the existing methodologies for phenological studies and the automation of the data flow between inputs and outputs with the use of different global free satellite datasets. In literature, many studies demonstrated the utility of the NDVI (Normalized Difference Vegetation Index) indices for the monitoring of vegetation dynamics, in the study of cultivations, and for the survey of the vegetation water stress. The author developed a procedure for creating layers of phenological parameters which integrates the TIMESAT software, produced by Lars Eklundh and Per Jönsson, for processing NDVI indices derived from different satellite sensors: MODIS (Moderate Resolution Imaging Spectroradiometer), AVHRR (Advanced Very High Resolution Radiometer) AND SPOT (Système Pour l'Observation de la Terre) VEGETATION. The automated procedure starts from data downloading, calls in a batch mode the software and provides customized layers of phenological parameters such as the starting of the season or length of the season and many others