Using Deep Learning to Count Albatrosses from Space: Assessing Results in Light of Ground Truth Uncertainty

Deep learning enables satellite-based monitoring of large populations of terrestrial mammals across heterogeneous landscape

New satellite remote sensing and machine learning techniques offer untapped possibilities to monitor global biodiversity with unprecedented speed and precision. These efficiencies promise to reveal novel ecological insights at spatial scales which are germane to the management of populations and entire ecosystems. Here, we present a robust transferable deep learning pipeline to automatically locate and count large herds of migratory ungulates (wildebeest and zebra) in the Serengeti-Mara ecosystem using fine-resolution (38-50 cm) satellite imagery. The results achieve accurate detection of nearly 500,000 individuals across thousands of square kilometers and multiple habitat types, with an overall F1-score of 84.75% (Precision: 87.85%, Recall: 81.86%). This research demonstrates the capability of satellite remote sensing and machine learning techniques to automatically and accurately count very large populations of terrestrial mammals across a highly heterogeneous landscape. We also discuss the potential for satellite-derived species detections to advance basic understanding of animal behavior and ecology.

Annotating very high-resolution satellite imagery: A whale case study

The use of very high-resolution (VHR) optical satellites is gaining momentum in the field of wildlife monitoring, particularly for whales, as this technology is showing potential for monitoring the less studied regions. However, surveying large areas using VHR optical satellite imagery requires the development of automated systems to detect targets. Machine learning approaches require large training datasets of annotated images. Here we propose a standardised workflow to annotate VHR optical satellite imagery using ESRI ArcMap 10.8, and ESRI ArcGIS Pro 2.5., using cetaceans as a case study, to develop AI-ready annotations.•A step-by-step protocol to review VHR optical satellite images and annotate the features of interest.•A step-by-step protocol to create bounding boxes encompassing the features of interest.•A step-by-step guide to clip the satellite image using bounding boxes to create image chips.

Artificial intelligence for automated detection of large mammals creates path to upscale drone surveys

Imagery from drones is becoming common in wildlife research and management, but processing data efficiently remains a challenge. We developed a methodology for training a convolutional neural network model on large-scale mosaic imagery to detect and count caribou (Rangifer tarandus), compare model performance with an experienced observer and a group of naïve observers, and discuss the use of aerial imagery and automated methods for large mammal surveys. Combining images taken at 75 m and 120 m above ground level, a faster region-based convolutional neural network (Faster-RCNN) model was trained in using annotated imagery with the labels: "adult caribou", "calf caribou", and "ghost caribou" (animals moving between images, producing blurring individuals during the photogrammetry processing). Accuracy, precision, and recall of the model were 80%, 90%, and 88%, respectively. Detections between the model and experienced observer were highly correlated (Pearson: 0.96-0.99, P value < 0.05). The model was generally more effective in detecting adults, calves, and ghosts than naïve observers at both altitudes. We also discuss the need to improve consistency of observers' annotations if manual review will be used to train models accurately. Generalization of automated methods for large mammal detections will be necessary for large-scale studies with diverse platforms, airspace restrictions, and sensor capabilities.

Do you get what you see? Insights of using mAP to select architectures of pretrained neural networks for automated aerial animal detection

The vast amount of images generated by aerial imagery in the context of regular wildlife surveys nowadays require automatic processing tools. At the top of the mountain of different methods to automatically detect objects in images reigns deep learning's object detection. The recent focus given to this task has led to an influx of many different architectures of neural networks that are benchmarked against standard datasets like Microsoft's Common Objects in COntext (COCO). Performance on COCO, a large dataset of computer vision images, is given in terms of mean Average Precision (mAP). In this study, we use six pretrained networks to detect red deer from aerial images, three of which have never been used, to our knowledge, in a context of aerial wildlife surveys. We compare their performance along COCO's mAP and a common test metric in animal surveys, the F1-score. We also evaluate how dataset imbalance and background uniformity, two common difficulties in wildlife surveys, impact the performance of our models. Our results show that the mAP is not a reliable metric to select the best model to count animals in aerial images and that a counting-focused metric like the F1-score should be favored instead. Our best overall performance was achieved with Generalized Focal Loss (GFL). It scored the highest along both metrics, combining most accurate counting and localization (with average F1-score of 0.96 and 0.97 and average mAP scores of 0.77 and 0.89 on both datasets respectively) and is therefore very promising for future applications. While both imbalance and background uniformity improved the performance of our models, their combined effect had twice as much impact as the choice of architecture. This finding seems to confirm that the recent data-centric shift in the deep learning field could also lead to performance gains in wildlife surveys.

An overview of remote monitoring methods in biodiversity conservation

Conservation of biodiversity is critical for the coexistence of humans and the sustenance of other living organisms within the ecosystem. Identification and prioritization of specific regions to be conserved are impossible without proper information about the sites. Advanced monitoring agencies like the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) had accredited that the sum total of species that are now threatened with extinction is higher than ever before in the past and are progressing toward extinct at an alarming rate. Besides this, the conceptualized global responses to these crises are still inadequate and entail drastic changes. Therefore, more sophisticated monitoring and conservation techniques are required which can simultaneously cover a larger surface area within a stipulated time frame and gather a large pool of data. Hence, this study is an overview of remote monitoring methods in biodiversity conservation via a survey of evidence-based reviews and related studies, wherein the description of the application of some technology for biodiversity conservation and monitoring is highlighted. Finally, the paper also describes various transformative smart technologies like artificial intelligence (AI) and/or machine learning algorithms for enhanced working efficiency of currently available techniques that will aid remote monitoring methods in biodiversity conservation.

Semi-Supervised Segmentation for Coastal Monitoring Seagrass Using RPA Imagery

Intertidal seagrass plays a vital role in estimating the overall health and dynamics of coastal environments due to its interaction with tidal changes. However, most seagrass habitats around the globe have been in steady decline due to human impacts, disturbing the already delicate balance in the environmental conditions that sustain seagrass. Miniaturization of multi-spectral sensors has facilitated very high resolution mapping of seagrass meadows, which significantly improves the potential for ecologists to monitor changes. In this study, two analytical approaches used for classifying intertidal seagrass habitats are compared—Object-based Image Analysis (OBIA) and Fully Convolutional Neural Networks (FCNNs). Both methods produce pixel-wise classifications in order to create segmented maps. FCNNs are an emerging set of algorithms within Deep Learning. Conversely, OBIA has been a prominent solution within this field, with many studies leveraging in-situ data and multiresolution segmentation to create habitat maps. This work demonstrates the utility of FCNNs in a semi-supervised setting to map seagrass and other coastal features from an optical drone survey conducted at Budle Bay, Northumberland, England. Semi-supervision is also an emerging field within Deep Learning that has practical benefits of achieving state of the art results using only subsets of labelled data. This is especially beneficial for remote sensing applications where in-situ data is an expensive commodity. For our results, we show that FCNNs have comparable performance with the standard OBIA method used by ecologists.

The Potential of Satellite Imagery for Surveying Whales

The emergence of very high-resolution (VHR) satellite imagery (less than 1 m spatial resolution) is creating new opportunities within the fields of ecology and conservation biology. The advancement of sub-meter resolution imagery has provided greater confidence in the detection and identification of features on the ground, broadening the realm of possible research questions. To date, VHR imagery studies have largely focused on terrestrial environments; however, there has been incremental progress in the last two decades for using this technology to detect cetaceans. With advances in computational power and sensor resolution, the feasibility of broad-scale VHR ocean surveys using VHR satellite imagery with automated detection and classification processes has increased. Initial attempts at automated surveys are showing promising results, but further development is necessary to ensure reliability. Here we discuss the future directions in which VHR satellite imagery might be used to address urgent questions in whale conservation. We highlight the current challenges to automated detection and to extending the use of this technology to all oceans and various whale species. To achieve basin-scale marine surveys, currently not feasible with any traditional surveying methods (including boat-based and aerial surveys), future research requires a collaborative effort between biology, computation science, and engineering to overcome the present challenges to this platform’s use.