Mário Cunha

Abstract
The spatial monitoring of plant diversity in the endangered species-rich grasslands of European mountain pastoral systems is an important step for fairer and more efficient Agri-Environmental policy schemes supporting conservation. This study assessed the underlying support for a spatially explicit monitoring of plant species richness at parcel level (policy making scale) in Southern European mountain grasslands, with statistical models informed by Sentinel-2 satellite and environmental factors. Twenty-four grassland parcels were surveyed for species richness in the Peneda-Gerês National Park, northern Portugal. Using a multi-model inference approach, three competing hypotheses guided by the species-scaling theoretical framework were established: species–area (P1), species–energy (P2) and species–spectral heterogeneity (P3), each representing a candidate spatial pathway to predict species richness. To evaluate the statistical support of each spatial pathway, generalized linear models were fitted and model selection based on Akaike information criterion (AIC) was conducted. Later, the performance of the most supported spatial pathway(s) was assessed using a leave-one-out cross validation. A model guided by the species–energy hypothesis (P2) was the most parsimonious spatial pathway to monitor plant species richness in mountain grassland parcels (P2, AICc = 137.6, ?AIC = 0.0, wi = 0.97). Species–area and species–spectral heterogeneity pathways (P1 and P3) were less statistically supported (?AICc values in the range 5.7–10.0). The underlying support of the species–energy spatial pathway was based on Sentinel-2 satellite data, namely on the near-infrared (NIR) green ratio in the spring season (NIR/Greenspring) and on its ratio of change between spring and summer (NIR/Greenchange). Both predictor variables related negatively to species richness. Grassland parcels with lower values of near-infrared (NIR) green ratio and lower seasonal amplitude presented higher species richness records. The leave-one-out cross validation indicated a moderate performance of the species–energy spatial pathway in predicting species richness in the grassland parcels covered by the dataset (R2 = 0.44, RMSE = 4.3 species, MAE = 3.5 species). Overall, a species–energy framework based on Sentinel 2 data resulted in a promising spatial pathway for the monitoring of species richness in mountain grassland parcels and for informing decision making on Agri-Environmental policy schemes. The near-infrared (NIR) green ratio and its change in time seems a relevant variable to deliver predictions for plant species richness and further research should be conducted on that.

Abstract
The harvesting operation is a recurring task in the production of any crop, thus making it an excellent candidate for automation. In protected horticulture, one of the crops with high added value is tomatoes. However, its robotic harvesting is still far from maturity. That said, the development of an accurate fruit detection system is a crucial step towards achieving fully automated robotic harvesting. Deep Learning (DL) and detection frameworks like Single Shot MultiBox Detector (SSD) or You Only Look Once (YOLO) are more robust and accurate alternatives with better response to highly complex scenarios. The use of DL can be easily used to detect tomatoes, but when their classification is intended, the task becomes harsh, demanding a huge amount of data. Therefore, this paper proposes the use of DL models (SSD MobileNet v2 and YOLOv4) to efficiently detect the tomatoes and compare those systems with a proposed histogram-based HSV colour space model to classify each tomato and determine its ripening stage, through two image datasets acquired. Regarding detection, both models obtained promising results, with the YOLOv4 model standing out with an F1-Score of 85.81%. For classification task the YOLOv4 was again the best model with an Macro F1-Score of 74.16%. The HSV colour space model outperformed the SSD MobileNet v2 model, obtaining results similar to the YOLOv4 model, with a Balanced Accuracy of 68.10%.

Abstract

Abstract
Roads and roadsides provide dispersal channels for non-native invasive alien plants (IAP), many of which hold devastating impacts in the economy, human health, biodiversity and ecosystem functionality. Remote sensing is an essential tool for efficiently assessing and monitoring the dynamics of IAP along roads. In this study, we explore the potentialities of object based image analysis (OBIA) approach to map several invasive plant species along roads using very high spatial resolution imagery. We compared the performance of OBIA approaches implemented in one open source software (OTB/Monteverdi) against those available in two proprietary pro-grams (eCognition and ArcGIS). We analysed the images by two sequential processes. First, we obtained a land-cover map for 15 study sites by segmenting the images with the algorithms Mean Shift Segmentation (MSS) and Multiresolution Segmentation (MRS), and by classifying the segmented images with the algorithms Support Vector Machine (SVM), Nearest Neighbour Classifier (NNC) and Maximum Likelihood Classifier (MLC). We created a mask using the polygons classified as non-vegetation to crop the images of the 15 study sites. Second, we repeated the previous segmentation and classification steps over the 15 masked images of vegetated areas using the same algorithms. OTB/Monteverdi, with MSS and SVM algorithms, showed to be a good software for land-cover mapping (OA = 87.0%), as well as ArcGIS, with MSS and MLC algorithms (OA = 84.3%). However, these two programs, using the same segmentation algorithms, did not achieve good accuracy results when mapping IAP species (OA(OTB/Monteverdi) = 63.3%; OAA(cos = 45.7%). eCognition, with MRS and NNC algorithms, reached better classification results in both land-cover and IAP maps (OA(Land-cover )= 95.7%; OA(Invasive-plant )= 92.8%). 'Bare soil' and 'Road', and 'A. donax' were the classes with best and worst overall accuracy, respectively, when mapping land-cover classes in the three programs. 'Other trees' was the class with the most accurate and significant differences in the three programs when mapping IAP species. The separation of each invasive species should be improved with a phenology-based design of field surveys. This study demonstrates the effectiveness of sequential segmentation and classification of RS data for mapping and monitoring plant invasions along linear infrastructures, which allows to reduce the time, cost and hazard of extensive field campaigns along roadsides.

Abstract
Wildfire disturbances can cause modifications in different dimensions of ecosystem functioning, i.e., the flows of matter and energy. There is an increasing need for methods to assess such changes, as functional approaches offer advantages over those focused solely on structural or compositional attributes. In this regard, remote sensing can support indicators for estimating a wide variety of effects of fire on ecosystem functioning, beyond burn severity assessment. These indicators can be described using intra-annual metrics of quantity, seasonality, and timing, called Ecosystem Functioning Attributes (EFAs). Here, we propose a satellite-based framework to evaluate the impacts, at short to medium term (i.e., from the year of fire to the second year after), of wildfires on four dimensions of ecosystem functioning: (i) primary productivity, (ii) vegetation water content, (iii) albedo, and (iv) sensible heat. We illustrated our approach by comparing inter-annual anomalies in satellite-based EFAs in the northwest of the Iberian Peninsula, from 2000 to 2018. Random Forest models were used to assess the ability of EFAs to discriminate burned vs. unburned areas and to rank the predictive importance of EFAs. Together with effect sizes, this ranking was used to select a parsimonious set of indicators for analyzing the main effects of wildfire disturbances on ecosystem functioning, for both the whole study area (i.e., regional scale), as well as for four selected burned patches with different environmental conditions (i.e., local scale). With both high accuracies (area under the receiver operating characteristic curve (AUC) > 0.98) and effect sizes (Cohen's |d| > 0.8), we found important effects on all four dimensions, especially on primary productivity and sensible heat, with the best performance for quantity metrics. Different spatiotemporal patterns of wildfire severity across the selected burned patches for different dimensions further highlighted the importance of considering the multi-dimensional effects of wildfire disturbances on key aspects of ecosystem functioning at different timeframes, which allowed us to diagnose both abrupt and lagged effects. Finally, we discuss the applicability as well as the potential advantages of the proposed approach for more comprehensive assessments of fire severity.