Forests are the planet’s main CO${}_2$ filtering agent as well as important economical, environmental and social assets. Climate change is exerting an increased stress, resulting in a need for improved research methodologies to study their health, composition or evolution. Traditionally, information about forests has been collected using expensive and work-intensive field inventories, but in recent years unoccupied autonomous vehicles (UAVs) have become very popular as they represent a simple and inexpensive way to gather high resolution data of large forested areas. In addition to this trend, deep learning (DL) has also been gaining much attention in the field of forestry as a way to include the knowledge of forestry experts into automatic software pipelines tackling problems such as tree detection or tree health/species classification. Among the many sensors that UAVs can carry, RGB cameras are fast, cost-effective and allow for straightforward data interpretation. This has resulted in a large increase in the amount of UAV-acquired RGB data available for forest studies. In this review, we focus on studies that use DL and RGB images gathered by UAVs to solve practical forestry research problems. We summarize the existing studies, provide a detailed analysis of their strengths paired with a critical assessment on common methodological problems and include other information, such as available public data and code resources that we believe can be useful for researchers that want to start working in this area. We structure our discussion using three main families of forestry problems: (1) individual Tree Detection, (2) tree Species Classification, and (3) forest Anomaly Detection (forest fires and insect Infestation).

3D registration or matching is a crucial step in 3D model reconstruction. Registration applications span along a variety of research fields, including computational geometry, computer vision, and geometric modeling. This variety of applications produces many diverse approaches to the problem but at the same time yields divergent notations and a lack of standardized algorithms and guidelines to classify existing methods. In this article, we review the state of the art of the 3D rigid registration topic (focused on Coarse Matching) and offer qualitative comparison between the most relevant approaches. Furthermore, we propose a pipeline to classify the existing methods and define a standard formal notation, offering a global point of view of the literature. Our discussion, based on the results presented in the analyzed papers, shows how, although certain aspects of the registration process still need to be tested further in real application situations, the registration pipeline as a whole has progressed steadily. As a result of this progress in all registration aspects, it is now possible to put together algorithms that are able to tackle new and challenging problems with unprecedented data sizes and meeting strict precision criteria.

Unmanned Aerial Vehicles (UAV) are becoming an essential tool for evaluating the status and the changes in forest ecosystems. This is especially important in Japan due to the sheer magnitude and complexity of the forest area, made up mostly of natural mixed broadleaf deciduous forests. Additionally, Deep Learning (DL) is becoming more popular for forestry applications because it allows for the inclusion of expert human knowledge into the automatic image processing pipeline. In this paper we study and quantify issues related to the use of DL with our own UAV-acquired images in forestry applications such as: the effect of Transfer Learning (TL) and the Deep Learning architecture chosen or whether a simple patch-based framework may produce results in different practical problems. We use two different Deep Learning architectures (ResNet50 and UNet), two in-house datasets (winter and coastal forest) and focus on two separate problem formalizations (Multi-Label Patch or MLP classification and semantic segmentation). Our results show that Transfer Learning is necessary to obtain satisfactory outcome in the problem of MLP classification of deciduous vs evergreen trees in the winter orthomosaic dataset (with a 9.78% improvement from no transfer learning to transfer learning from a a general-purpose dataset). We also observe a further 2.7% improvement when Transfer Learning is performed from a dataset that is closer to our type of images. Finally, we demonstrate the applicability of the patch-based framework with the ResNet50 architecture in a different and complex example: Detection of the invasive broadleaf deciduous black locust (Robinia pseudoacacia) in an evergreen coniferous black pine (Pinus thunbergii) coastal forest typical of Japan. In this case we detect images containing the invasive species with a 75% of True Positives (TP) and 9% False Positives (FP) while the detection of native trees was 95% TP and 10% FP.

Insect outbreaks are a recurrent natural phenomenon in forest ecosystems expected to increase due to climate change. Recent advances in Unmanned Aerial Vehicles (UAV) and Deep Learning (DL) Networks provide us with tools to monitor them. In this study we used nine orthomosaics and normalized Digital Surface Models (nDSM) to detect and classify healthy and sick Maries fir trees as well as deciduous trees. This study aims at automatically classifying treetops by means of a novel computer vision treetops detection algorithm and the adaptation of existing DL architectures. Considering detection alone, the accuracy results showed 85.70% success. In terms of detection and classification, we were able to detect/classify correctly 78.59% of all tree classes (39.64% for sick fir). However, with data augmentation, detection/classification percentage of the sick fir class rose to 73.01% at the cost of the result accuracy of all tree classes that dropped 63.57%. The implementation of UAV, computer vision and DL techniques contribute to the development of a new approach to evaluate the impact of insect outbreaks in forest.

Breast magnetic resonance imaging (MRI) and x‐ray mammography are two image modalities widely used for the early detection and diagnosis of breast diseases in women. The combination of these modalities leads to a more accurate diagnosis and treatment of breast diseases. The aim of this paper is to review the registration between breast MRI and x‐ray mammographic images using patient‐specific finite element‐based biomechanical models. Specifically, a biomechanical model is obtained from the patient's MRI volume and is subsequently used to mimic the mammographic acquisition. Due to the different patient positioning and movement restrictions applied in each image modality, the finite element analysis provides a realistic physics‐based approach to perform the breast deformation. In contrast with other reviews, we do not only expose the overall process of compression and registration but we also include main ideas, describe challenges, and provide an overview of the used software in each step of the process. Extracting an accurate description from the MR images and preserving the stability during the finite element analysis require an accurate knowledge about the algorithms used, as well as the software and underlying physics. The wide perspective offered makes the paper suitable not only for expert researchers but also for graduate students and clinicians. We also include several medical applications in the paper, with the aim to fill the gap between the engineering and clinical performance.