Remote Sensing of Land Surface Phenology

Land surface phenology (LSP) uses remote sensing to monitor seasonal dynamics in vegetated land surfaces and retrieve phenological metrics (transition dates, rate of change, annual integrals, etc.). LSP has developed rapidly in the last few decades. Both regional and global LSP products have been routinely generated and play prominent roles in modeling crop yield, ecological surveillance, identifying invasive species, modeling the terrestrial biosphere, and assessing impacts on urban and natural ecosystems. Recent advances in field and spaceborne sensor technologies, as well as data fusion techniques, have enabled novel LSP retrieval algorithms that refine retrievals at even higher spatiotemporal resolutions, providing new insights into ecosystem dynamics. Meanwhile, rigorous assessment of the uncertainties in LSP retrievals is ongoing, and efforts to reduce these uncertainties represent an active research area. Open source software and hardware are in development, and have greatly facilitated the use of LSP metrics by scientists outside the remote sensing community. This reprint covers the latest developments in sensor technologies, LSP retrieval algorithms and validation strategies, and the use of LSP products in a variety of fields. It aims to summarize the ongoing diverse LSP developments and boost discussions on future research prospects

Mapping of multitemporal rice (Oryza sativa L.) growth stages using remote sensing with multi-sensor and machine learning : a thesis dissertation presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Earth Science at Massey University, Manawatū, New Zealand

Figure 2.1 is adapted and re-used under a Creative Commons Attribution 4.0 International (CC BY 4.0) license.Rice (Oryza Sativa) plays a pivotal role in food security for Asian countries, especially in Indonesia. Due to the increasing pressure of environmental changes, such as land use and climate, rice cultivation areas need to be monitored regularly and spatially to ensure sustainable rice production. Moreover, timely information of rice growth stages (RGS) can lead to more efficient of inputs distribution from water, seed, fertilizer, and pesticide. One of the efficient solutions for regularly mapping the rice crop is using Earth observation satellites. Moreover, the increasing availability of open access satellite images such as Landsat-8, Sentinel-1, and Sentinel-2 provides ample opportunities to map continuous and high-resolution rice growth stages with greater accuracy. The majority of the literature has focused on mapping rice area, cropping patterns and relied mainly on the phenology of vegetation. However, the mapping process of RGS was difficult to assess the accuracy, time-consuming, and depended on only one sensor. In this work, we discuss the use of machine learning algorithms (MLA) for mapping paddy RGS with multiple remote sensing data in near-real-time. The study area was Java Island, which is the primary rice producer in Indonesia. This study has investigated: (1) the mapping of RGS using Landsat-8 imagery and different MLAs, and their rigorous performance was evaluated by conducting a multitemporal analysis; (2) the temporal consistency of predicting RGS using Sentinel-2, MOD13Q1, and Sentinel-1 data; (3) evaluating the correlation of local statistics data and paddy RGS using Sentinel-2, PROBA-V, and Sentinel-1 with MLAs. The ground truth datasets were collected from multi-year web camera data (2014-2016) and three months of the field campaign in different regions of Java (2018). The study considered the RGS in the analysis to be vegetative, reproductive, ripening, bare land, and flooding, and MLAs such as support vector machines (SVMs), random forest (RF), and artificial neural network (ANN) were used. The temporal consistency matrix was used to compare the classification maps within three sensor datasets (Landsat-8 OLI, Sentinel-2, and Sentinel-2, MOD13Q1, Sentinel-1) and in four periods (5, 10, 15, 16 days). Moreover, the result of the RGS map was also compared with monthly data from local statistics within each sub-district using cross-correlation analysis. The result from the analysis shows that SVM with a radial base function outperformed the RF and ANN and proved to be a robust method for small-size datasets (< 1,000 points). Compared to Sentinel-2, Landsat-8 OLI gives less accuracy due to the lack of a red-edge band and larger pixel size (30 x 30 m). Integration of Sentinel-2, MOD13Q1, and Sentinel-1 improved the classification performance and increased the temporal availability of cloud-free maps. The integration of PROBA-V and Sentinel-1 improved the classification accuracy from the Landsat-8 result, consistent with the monthly rice planting area statistics at the sub-district level. The western area of Java has the highest accuracy and consistency since the cropping pattern only relied on rice cultivation. In contrast, less accuracy was noticed in the eastern area because of upland rice cultivation due to limited irrigation facilities and mixed cropping. In addition, the cultivation of shallots to the north of Nganjuk Regency interferes with the model predictions because the cultivation of shallots resembles the vegetative phase due to the water banks. One future research idea is the auto-detection of the cropping index in the complex landscape to be able to use it for mapping RGS on a global scale. Detection of the rice area and RGS using Google Earth Engine (GEE) can be an action plan to disseminate the information quickly on a planetary scale. Our results show that the multitemporal Sentinel-1 combined with RF can detect rice areas with high accuracy (>91%). Similarly, accurate RGS maps can be detected by integrating multiple remote sensing (Sentinel-2, Landsat-8 OLI, and MOD13Q1) data with acceptable accuracy (76.4%), with high temporal frequency and lower cloud interference (every 16 days). Overall, this study shows that remote sensing combined with the machine learning methodology can deliver information on RGS in a timely fashion, which is easy to scale up and consistent both in time and space and matches the local statistics. This thesis is also in line with the existing rice monitoring projects such as Crop Monitor, Crop Watch, AMIS, and Sen4Agri to support disseminating information over a large area. To sum up, the proposed workflow and detailed map provide a more accurate method and information in near real-time for stakeholders, such as governmental agencies against the existing mapping method. This method can be introduced to provide accurate information to rice farmers promptly with sufficient inputs such as irrigation, seeds, and fertilisers for ensuring national food security from the shifting planting time due to climate change

Crop growth and yield monitoring in smallholder agricultural systems:a multi-sensor data fusion approach

Smallholder agricultural systems are highly vulnerable to production risks posed by the intensification of extreme weather events such as drought and flooding, soil degradation, pests, lack of access to agricultural inputs, and political instability. Monitoring the spatial and temporal variability of crop growth and yield is crucial for farm management, national-level food security assessments, and famine early warning. However, agricultural monitoring is difficult in fragmented agricultural landscapes because of scarcity and uncertainty of data to capture small crop fields. Traditional pre- and post-harvest crop monitoring and yield estimation based on fieldwork is costly, slow, and can be unrepresentative of heterogeneous agricultural landscapes as found in smallholder systems in sub-Saharan Africa. Devising accurate and timely crop phenology detection and yield estimation methods can improve our understanding of the status of crop production and food security in these regions.Satellite-based Earth observation (EO) data plays a key role in monitoring the spatial and temporal variability of crop growth and yield over large areas. The small field sizes and variability in management practices in fragmented landscapes requires high spatial and high temporal resolution EO data. This thesis develops and demonstrates methods to investigate the spatiotemporal variability of crop phenology detection and yield estimation using Landsat and MODIS data fusion in smallholder agricultural systems in the Lake Tana sub-basin of Ethiopia. The overall aim is to further broaden the application of multi-sensor EO data for crop growth monitoring in smallholder agricultural systems.The thesis addressed two important aspects of crop monitoring applications of EO data: phenology detection and yield estimation. First, the ESTARFM data fusion workflow was modified based on local knowledge of crop calendars and land cover to improve crop phenology monitoring in fragmented agricultural landscapes. The approach minimized data fusion uncertainties in predicting temporal reflectance change of crops during the growing season and the reflectance value of fused data was comparable to the original Landsat image reserved for validation. The main sources of uncertainty in data fusion are the small field size and abrupt crop growth changes between the base andviiprediction dates due to flooding, weeding, fertiliser application, and harvesting. The improved data fusion approach allowed us to determine crop phenology and estimate LAI more accurately than both the standard ESTARFM data fusion method and when using MODIS data without fusion. We also calibrated and validated a dynamic threshold phenology detection method using maize and rice crop sowing and harvest date information. Crop-specific phenology determined from data fusion minimized the mismatch between EO-derived phenometrics and the actual crop calendar. The study concluded that accurate phenology detection and LAI estimation from Landsat–MODIS data fusion demonstrates the feasibility of crop growth monitoring using multi-sensor data fusion in fragmented and persistently cloudy agricultural landscapes.Subsequently, the validated data fusion and phenology detection methods were implemented to understand crop phenology trends from 2000 to 2020. These trends are often less understood in smallholder agricultural systems due to the lack of high spatial resolution data to distinguish crops from the surrounding natural vegetation. Trends based on Landsat–MODIS fusion were compared with those detected using MODIS alone to assess the contribution of data fusion to discern crop phenometric change. Landsat and MODIS fusion discerned crop and environment-specific trends in the magnitude and direction of crop phenology change. The results underlined the importance of high spatial and temporal resolution EO data to capture environment-specific crop phenology change, which has implications in designing adaptation and crop management practices in these regions.The second important aspect of the crop monitoring problem addressed in this thesis is improving crop yield estimation in smallholder agricultural systems. The large input requirements of crop models and lack of spatial information about the heterogeneous crop-growing environment and agronomic management practices are major challenges to the accurate estimation of crop yield. We assimilated leaf area index (LAI) and phenology information from Landsat–MODIS fusion in a crop model (simple algorithm for yield estimation: SAFY) to obtain reasonably reliable crop yield estimates. The SAFY model is sensitive to the spatial and temporal resolution of the calibration input LAI, phenology information, and the effective light use efficiency (ELUE) parameter, which needs accurate field level inputs during modelviiioptimization. Assimilating fused EO-based phenology information minimized model uncertainty and captured the large management and environmental variation in smallholder agricultural systems.In the final research chapter of the thesis, we analysed the contribution of assimilating LAI at different phenological stages. The frequency and timing of LAI observations influences the retrieval accuracy of the assimilating LAI in crop growth simulation models. The use of (optical) EO data to estimate LAI is constrained by limited repeat frequency and cloud cover, which can reduce yield estimation accuracy. We evaluated the relative contribution of EO observations at different crop growth stages for accurate calibration of crop model parameters. We found that LAI between jointing and grain filling has the highest contribution to SAFY yield estimation and that the distribution of LAI during the key development stages was more useful than the frequency of LAI to improve yield estimation. This information on the optimal timing of EO data assimilation is important to develop better in-season crop yield forecasting in smallholder systems

Drought impacts assessment in Brazil - a remote sensing approach

Climate extremes are becoming more frequent in Brazil; studies project an increase in drought occurrences in many regions of the country. In the south, drought events lead to crop yield losses affecting the value chain and, therefore, the local economy. In the northeast, extended periods of drought lead to potential land degradation, affecting the livelihood and hindering local development. In the southern Amazon, an area that experienced intense land use change (LUC) in the last, the impacts are even more complex, ranging from crop yield loss and forest resilience loss, affecting ecosystem health and putting a threat on the native population traditional way of living. In the studies here we analyzed the drought impacts in these regions during the 2000s, which vary in nature and outcomes. We addressed some of the key problems in each of the three regions: i) for the southern agriculture, we tackled the problem of predicting soybean yield based on within-season remote sensing (RS) data, ii) in the northeast we mapped areas presenting trends of land degradation in the wake of an extended drought and, iii) in southern Amazon, we characterized a complex degradation cycle encompassing LUC, fire occurrence, forest resilience loss, carbon balance, and the interconnectedness of these factors impacting the local climate. Advisor: Brian D. Wardlo

EVALUATING THE RELATIVE CONTRIBUTION OF CHANGING FARMING METHODS TO HABITAT LOSS IN THE MID-ZAMBEZI VALLEY, ZIMBABWE

Agriculture expansion is a major contributor to wildlife habitat loss in the ecological frontier areas. However, little is known about the contribution of different crops to wildlife habitat loss. In this study we evaluated the relative contribution of changes in farming practices, particularly the introduction of cotton (Gossypium hirsutum L) to the loss of wildlife habitat with specific focus on the African elephant (Loxodonta africana) in the mid- Zambezi Valley, Zimbabwe. First, we developed a remote sensing method based on normalised difference vegetation index (NDVI) derived from 16 day multi-temporal Moderate Resolution Imaging Spectroradiometer (MODIS) remotely sensed data for the 2007 growing period, to test whether cotton (Gossypium hirsutum L) fields can significantly (p < 0.05) be distinguished from maize (Zea mays L) fields, as well as sorghum (Sorghum bicolor) fields. Second, we tested whether woodland fragmentation in the study area was best explained by the areal extent of cotton fields than the areal extent of cereal fields. Finally, we tested whether woodland fragmentation resulting from cotton fields explains elephant distribution better than woodland fragmentation resulting from the extent of cereal fields. Results show that multi-temporal remotely sensed data can be used to distinguish and map cotton and cereal fields. Cotton fields contributed more to woodland fragmentation than cereal fields. Also, we found out that woodland fragmentation from cotton fields significantly explained elephant distribution in the mid- Zambezi Valley. These results indicate that the areal extent of cotton fields explains elephant habitat fragmentation more than the areal extent of cereal fields. Thus, we conclude that the expansion of cotton fields contributes most to elephant habitat loss in the Mid-Zambezi Valley. These results imply that elephant conservation policy needs to address the reduction of the negative impact of cash crops such as cotton on the habitat particularly their threat to wildlife habitat which may eventually lead to loss these wild animals. Thus it is important to strike a balance between wildlife habitat conservation and agricultural production as advocated through the Communal Areas Management Programme For Indigenous Resources (CAMPFIRE) polic

Augmenting Land Cover/Land Use Classification by Incorporating Information from Land Surface Phenology: An Application to Quantify Recent Cropland Expansion in South Dakota

Understanding rapid land change in the U.S. NGP region is not only critical for management and conservation of prairie habitats and ecosystem services, but also for projecting production of crops and biofuels and the impacts of land conversion on water quality and rural transportation infrastructure. Hence, it raises the need for an LCLU dataset with good spatiotemporal coverage as well as consistent accuracy through time to enable change analysis. This dissertation aims (1) to develop a novel classification method, which utilizes time series images from comparable sensors, from the perspective of land surface phenology, and (2) to apply the land cover/land use dataset generated from the phenometrically-based classification approach to quantify crop expansion in South Dakota. A novel classification approach from the perspective of land surface phenology (LSP) uses rich time series datasets. First, surface reflectance products at 30 m spatial resolution from Landsat Collection-1, its newer structure—Landsat Analysis Ready Data, and the Harmonized Landsat Sentinel-2 (HLS) data are used to construct vegetation index time series, including the Enhanced Vegetation Index (EVI), and the 2-band EVI (EVI2), and various spectral variables (spectral band and normalized ratio composites). MODIS Level-3 Land Surface Temperature & Emissivity 8-day composite products at 1 km spatial resolution from both the Aqua and Terra satellites are used to compute accumulated growing degree-days (AGDD) time series. The EVI/EVI2 and AGDD time series are then fitted by two different land surface phenology models: the Convex Quadratic model and the Hybrid Piecewise Logistic Model. Suites of phenometrics are derived from the two LSP models and spectral variables and input to Random Forest Classifiers (RFC) to map land cover of sample areas in South Dakota. The results indicate that classifications using only phenometrics can accurately map major crops in the study area but show limited accuracy for non-vegetated land covers. RFC models using the combined spectralphenological variables can achieve higher accuracies than those using either spectral variables or phenometrics alone, especially for the barren/developed class. Among all sampling designs, the “same distribution” models—proportional distribution of the sample is like proportional distribution of the population—tends to yield best land cover prediction. A “same distribution” random sample dataset covering approximately 0.25% or more of the study area appears to achieve an accurate land cover map. To characterize crop expansion in South Dakota, a trajectory-based analysis, which considers the entire land cover dataset generated from the LSP-based classifications, is proposed to improve change detection. An estimated cropland expansion of 5,447 km2 (equivalent to 14% of the existing cropland area) occurred between 2007 and 2015, which matches more closely the reports from the National Agriculture Statistics Service—NASS (5,921 km2) and the National Resources Inventory—NRI (5,034 km2) than an estimation from a bi-temporal change approach (8,018 km2). Cropland gains were mostly concentrated in 10 counties in northern and central South Dakota. An evaluation of land suitability for crops using the Soil Survey Geographic Database—SSURGO indicates a scarcity in high-quality arable land available for cropland expansion

Spatio-temporal Analysis of Agriculture in the Vietnamese Mekong Delta using MODIS Imagery

New methodologies using MODIS time‒series imagery were developed for revealing spatio‒temporal changes of agricultural environments and land use patterns in the Vietnamese Mekong Delta. The following methodologies were proposed:a Wavelet based Filter for Crop Phenology (WFCP), a Wavelet‒based fi lter for evaluating the spatial distribution of Cropping Systems (WFCS), and a Wavelet‒based fi lter for detecting spatio‒temporal changes in Flood Inundation(WFFI). The WFCP algorithm involves smoothing the temporal profi le of the Enhanced Vegetation Index (EVI) using the wavelet transform approach. As a result of validation using the agricultural statistical data in Japan, it was shown that the WFCP was able to estimate rice growing stages, including transplanting date, heading date and harvesting date from the smoothed EVI data, with 9‒12 days accuracy(RMSE). The WFCS algorithm was developed for detecting rice‒cropping patterns in the Vietnamese Mekong delta based on WFCP. It was revealed that the spatial distribution of rice cropping seasons was characterized by both annual fl ood inundation around the upper region in the rainy season and salinity intrusion around the coastal region in the dry season. The WFFI algorithm was developed for estimating start and end dates of fl ood inundation by using time‒series Land Surface Water Index and EVI. Annual intensity of Mekong fl oods was evaluated from 2000 to 2004, at a regional scale. Applying a series of wavelet‒based methodologies to the MODIS data acquired from 2000 to 2006, it was confi rmed that the cropping season for the winter‒spring rice in the fl ood‒prone area fl uctuated depending on the annual change of fl ood scale. It was also confi rmed that the triple rice‒cropped area in the An Giang province expanded from 2000 to 2005, because the construction of a ring‒dike system and water‒resource infrastructure made it possible to sustain a third rice cropping season during the fl ood season. The proposed methodologies(WFCP, WFCS, WFFI) based on MODIS time‒series imagery made it clear that while the rice cropping in the Vietnamese Mekong Delta was quantitatively(annual fl ooding) and qualitatively(salinity intrusion) affected by water‒resource changes, there were some regions where the cultivation system was changed from double rice cropping to triple rice cropping because of the implementation of measures against fl ooding.日本の食料自給率 (2005年時の供給熱量ベース) は、40% と先進7カ国の中で最も低い。日本は、その食料海外依存度の高さから、世界的な食料価格の変動の影響を最も受け易い国と言える。近年の経済発展に伴う中国の大豆輸入量の増加や世界的なエネルギー政策の転換 (バイオエタノール政策) は、世界の穀物需給バランスを不安定にさせつつあり、世界的な問題となっている。さらに、地球温暖化による農業生産影響、増加し続ける世界人口、鈍化する穀物生産性を考えれば、世界の食料需給バランスが将来にわたって安定し続けると言うことはできないだろう。他方、食料増産・生産性向上を目的とした集約的農業の展開は、発展途上国の農業環境にさらなる負荷を与えるかもしれない。世界の食料生産と密接な関係にある日本は、自国の食料安全保障を議論する前提として、急速に変わり行く世界の農業生産現場やそれを取り巻く農業環境を客観的に理解し、世界の農業環境情報を独自の手法によって収集・整理する必要がある。そこで、筆者は、衛星リモートセンシング技術を活用することによって、地球規模の視点で、時間的・空間的な広がりを持って変わり行く農業生産活動とそれを取り巻く農業環境情報を把握・理解するための時系列衛星データ解析手法の確立を目指すこととした。本研究では、インドシナ半島南端に位置するベトナム・メコンデルタを調査対象領域とした。ベトナムは、タイに次ぐ世界第2位のコメ輸出国であり、その輸出米の9割近くが、ベトナム・メコンデルタで生産されたものである。筆者は、ベトナム・メコンデルタを世界の食料安全保障を考える上で重要な食料生産地帯の一つであると考え、本地域における農業環境及び土地利用パターンの時空間変化を明らかにするためのMODIS データを用いた新たな時系列解析手法の開発を行った。　本研究において提案する時系列解析手法は、次の三つである。1. Wavelet‒based Filter for Crop Phenology (WFCP) ,2. Wavelet‒based Filter for evaluating the spatial distribution of Cropping System (WFCS) , 3. Wavelet‒based Filterfor detecting spatio‒temporal changes in Flood Inundation (WFFI) . WFCP は、時系列植生指数 (EVI) を平滑化するためにウェーブレット変換手法を利用しており、日本の農業統計データを用いた検証結果から、水稲生育ステージ (田植日、出穂日、収獲日) を約9－12日 (RMSE) の精度で推定可能であることが示された。WFCP を基に改良されたWFCS は、水稲作付パターンの年次把握を可能にし、ベトナムメコンデルタにおける水稲作付時期の空間分布が、上流部において毎年雨期に発生する洪水と沿岸部において乾季に発生する塩水遡上によって特徴づけられていることを明らかにした。WFFI は、時系列水指数 (LSWI) と植生指数 (EVI) から、湛水期間、湛水開始日・湛水終息日を広域把握し、メコン川洪水強度の年次変化を地域スケールで評価することを可能にする。そして、ウェーブレット変換を利用した一連の手法を、2000～2006年までのMODIS 時系列画像に適用することによって、メコンデルタ上流部の洪水常襲地帯において、冬春米の作付時期が、年次変化する洪水規模に依存していることを明らかにした。また、An Giang 省において、堤防建設 (輪中) や水利施設の建設によって、洪水期における水稲三期作が可能になった地域が、2000～2005年にかけて拡大していることを明らかにした。本研究で提案したMODIS 時系列画像を利用した時系列解析手法 (WFCP、WFCS、WFFI) によって、ベトナムメコンデルタにおける水稲生産が水資源の量的 (洪水) ・質的 (塩水遡上) 変動影響を受ける一方、洪水対策の実施によって、栽培体系を二期作から三期作に変更している地域があることを明らかにした

Applications of satellite ‘hyper-sensing’ in Chinese agriculture:Challenges and opportunities

Ensuring adequate food supplies to a large and increasing population continues to be the key challenge for China. Given the increasing integration of China within global markets for agricultural products, this issue is of considerable significance for global food security. Over the last 50 years, China has increased the production of its staple crops mainly by increasing yield per unit land area. However, this has largely been achieved through inappropriate agricultural practices, which have caused environmental degradation, with deleterious consequences for future agricultural productivity. Hence, there is now a pressing need to intensify agriculture in China using practices that are environmentally and economically sustainable. Given the dynamic nature of crops over space and time, the use of remote sensing technology has proven to be a valuable asset providing end-users in many countries with information to guide sustainable agricultural practices. Recently, the field has experienced considerable technological advancements reflected in the availability of ‘hyper-sensing’ (high spectral, spatial and temporal) satellite imagery useful for monitoring, modelling and mapping of agricultural crops. However, there still remains a significant challenge in fully exploiting such technologies for addressing agricultural problems in China. This review paper evaluates the potential contributions of satellite ‘hyper-sensing’ to agriculture in China and identifies the opportunities and challenges for future work. We perform a critical evaluation of current capabilities in satellite ‘hyper-sensing’ in agriculture with an emphasis on Chinese sensors. Our analysis draws on a series of in-depth examples based on recent and on-going projects in China that are developing ‘hyper-sensing’ approaches for (i) measuring crop phenology parameters and predicting yields; (ii) specifying crop fertiliser requirements; (iii) optimising management responses to abiotic and biotic stress in crops; (iv) maximising yields while minimising water use in arid regions; (v) large-scale crop/cropland mapping; and (vi) management zone delineation. The paper concludes with a synthesis of these application areas in order to define the requirements for future research, technological innovation and knowledge exchange in order to deliver yield sustainability in China