Modeling Habitat Suitability of Migratory Birds from Remote Sensing Images Using Convolutional Neural Networks

Machine and deep learning approaches to understand and predict habitat suitability for seabird breeding

The way animals select their breeding habitat may have great impacts on individual fitness. This complex process depends on the integration of information on various environmental factors, over a wide range of spatiotemporal scales. For seabirds, breeding habitat selection integrates both land and sea features over several spatial scales. Seabirds explore these features prior to breeding, assessing habitats' quality. However, the information-gathering and decision-making process by seabirds when choosing a breeding habitat remains poorly understood. We compiled 49 historical records of larids colonies in Cuba from 1980 to 2020. Then, we predicted potentially suitable breeding sites for larids and assessed their breeding macrohabitat selection, using deep and machine learning algorithms respectively. Using a convolutional neural network and Landsat satellite images we predicted the suitability for nesting of non-monitored sites of this archipelago. Furthermore, we assessed the relative contribution of 18 land- and marine-based environmental covariates describing macrohabitats at three spatial scales (i.e. 10, 50 and 100 km) using random forests. Convolutional neural network exhibited good performance at training, validation and test (F1-scores >85%). Sites with higher habitat suitability (p > .75) covered 20.3% of the predicting area. Larids breeding macrohabitats were sites relatively close to main islands, featuring sparse vegetation cover and high chlorophyll-a concentration at sea in 50 and 100 km around colonies. Lower sea surface temperature at larger spatial scales was determinant to distinguish the breeding from non-breeding sites. A more comprehensive understanding of the seabird breeding macrohabitats selection can be reached from the complementary use of convolutional neural networks and random forest models. Our analysis provides crucial knowledge in tropical regions that lack complete and regular monitoring of seabirds' breeding sites.

Erythrocyte micronucleus cytome assay in Passer domesticus and environmental remote sensing for inferring the quality of wild, rural, and urban areas

The study of biomarkers in free-living birds can help to indicate the degree of contamination in distinct environments. In addition, these environments can be characterized through the information provided by satellite images. The objectives of the present study were to analyze the types and quantity of cytogenetic biomarkers in Passer domesticus (House sparrow) from three different environments, wild, rural, and urban, and to analyze them in the context of land use and anthropogenic actions. Five thousand erythrocytes per bird were analyzed for the following nuclear alterations (NA): micronuclei (MN), nuclear buds, notched nuclei, binucleated cells, nucleoplasmic bridges, nuclear tails, peripheral nuclei, and anucleated cells. In the study, wild birds exhibited five types of NA, seven types were found in rural birds, and all types were encountered in urban birds. The only NA that exceeded a frequency of 2 NA/1000 erythrocytes were peripheral nuclei in birds from the rural and urban sites, the latter environment characterized by 87% urban soil and air pollution. The highest frequencies of MN, peripheral nuclei, and anucleated erythrocytes were recorded in sparrows from the rural site (p ≤ 0.05). This area had been sprayed with chlorpyrifos 48%, the most widely used organophosphate in the region. Sparrows from the wild site, made up of 100% native forest, had higher frequencies of notched nuclei (p ≤ 0.05). A precedent is set for the use of environmental remote sensing in a complementary manner with cytogenetic biomarker studies in birds for a joint analysis in environmental assessment.

Efficient Detection Method of Pig-Posture Behavior Based on Multiple Attention Mechanism

Due to the low detection precision and poor robustness, the traditional pig-posture and behavior detection method is difficult to apply in the complex pig captivity environment. In this regard, we designed the HE-Yolo (High-effect Yolo) model, which improves the Darknet-53 feature extraction network and integrates DAM (Dual attention mechanism) of channel attention mechanism and space attention mechanism, to recognize the posture behaviors of the enclosure pigs in real-time. First, the pig data set is clustered and optimized by the K-means algorithm to obtain a new anchor frame size. Second, the DSC (Depthwise separable convolution) and h-switch activation function are innovatively introduced into the Darknet-53 feature extraction network, and the C-Res (Contrary residual structure) unit is designed to build Darknet-A feature extraction network, so as to avoid network gradient explosion and ensure the integrity of feature information. Subsequently, DAM integrating the spatial attention mechanism and the channel attention mechanism is established, and it is further combined with the Incep-abate module to form DAB (Dual attention block), and HE-Yolo is finally built by Darknet-A and DAB. A total of 2912 images of 46 enclosure pigs are divided into the training set, the verification set, and the test set according to the ratio of 14 : 3:3, and the recognition performance of HE-Yolo is verified according to the parameters of the precision P, the recall R, the AP (i.e., the area of P-R curve) and the MAP (i.e., the average value of AP). The experiment results show that the AP values of HE-Yolo reach 99.25%, 98.41%, 94.43%, and 97.63%, respectively, in the recognition of four pig-posture behaviors of standing, sitting, prone and sidling of the test set. Compared with other models such as Yolo v3, SSD, and faster R–CNN, the mAP value of HE-Yolo is increased by 5.61%, 4.65%, and 0.57%, respectively, and the single-frame recognition time of HE-Yolo is only 0.045 s. In the recognition of images with foreign body occlusion and pig adhesion, the mAP values of HE-Yolo are increased by 4.04%, 4.94%, and 1.76%, respectively, while compared with other models. Under different lighting conditions, the mAP value of HE-Yolo is also higher than that of other models. The experimental results show that HE-Yolo can recognize the pig-posture behaviors with high precision, and it shows good generalization ability and luminance robustness, which provides technical support for the recognition of pig-posture behaviors and real-time monitoring of physiological health of the enclosure pigs.

Whale counting in satellite and aerial images with deep learning

Despite their interest and threat status, the number of whales in world’s oceans remains highly uncertain. Whales detection is normally carried out from costly sighting surveys, acoustic surveys or through high-resolution images. Since deep convolutional neural networks (CNNs) are achieving great performance in several computer vision tasks, here we propose a robust and generalizable CNN-based system for automatically detecting and counting whales in satellite and aerial images based on open data and tools. In particular, we designed a two-step whale counting approach, where the first CNN finds the input images with whale presence, and the second CNN locates and counts each whale in those images. A test of the system on Google Earth images in ten global whale-watching hotspots achieved a performance (F1-measure) of 81% in detecting and 94% in counting whales. Combining these two steps increased accuracy by 36% compared to a baseline detection model alone. Applying this cost-effective method worldwide could contribute to the assessment of whale populations to guide conservation actions. Free and global access to high-resolution imagery for conservation purposes would boost this process.