Distortion Correction and Denoising of Light Sheet Fluorescence Images.

Light Sheet Fluorescence Microscopy (LSFM) has emerged as a valuable tool for neurobiologists, enabling the rapid and high-quality volumetric imaging of mice brains. However, inherent artifacts and distortions introduced during the imaging process necessitate careful enhancement of LSFM images for optimal 3D reconstructions. This work aims to correct images slice by slice before reconstructing 3D volumes. Our approach involves a three-step process: firstly, the implementation of a deblurring algorithm using the work of K. Becker; secondly, an automatic contrast enhancement; and thirdly, the development of a convolutional denoising auto-encoder featuring skip connections to effectively address noise introduced by contrast enhancement, particularly excelling in handling mixed Poisson-Gaussian noise. Additionally, we tackle the challenge of axial distortion in LSFM by introducing an approach based on an auto-encoder trained on bead calibration images. The proposed pipeline demonstrates a complete solution, presenting promising results that surpass existing methods in denoising LSFM images. These advancements hold potential to significantly improve the interpretation of biological data.

Fusion between an Algorithm Based on the Characterization of Melanocytic Lesions' Asymmetry with an Ensemble of Convolutional Neural Networks for Melanoma Detection.

Melanoma is still a major health problem worldwide. Early diagnosis is the first step toward reducing its mortality, but it remains a challenge even for experienced dermatologists. Although computer-aided systems have been developed to help diagnosis, the lack of insight into their predictions is still a significant limitation toward acceptance by the medical community. To tackle this issue, we designed handcrafted expert features representing color asymmetry within the lesions, which are parts of the approach used by dermatologists in their daily practice. These features are given to an artificial neural network classifying between nevi and melanoma. We compare our results with an ensemble of 7 state-of-the-art convolutional neural networks and merge the 2 approaches by computing the average prediction. Our experiments are done on a subset of the International Skin Imaging Collaboration 2019 dataset (6296 nevi, 1361 melanomas). The artificial neural network based on asymmetry achieved an area under the curve of 0.873, sensitivity of 90%, and specificity of 67%; the convolutional neural network approach achieved an area under the curve of 0.938, sensitivity of 91%, and specificity of 82%; and the fusion of both approaches achieved an area under the curve of 0.942, sensitivity of 92%, and specificity of 82%. Merging the knowledge of dermatologists with convolutional neural networks showed high performance for melanoma detection, encouraging collaboration between computer science and medical fields.

Computer Aided Diagnosis of Melanoma Using Deep Neural Networks and Game Theory: Application on Dermoscopic Images of Skin Lesions.

Early detection of melanoma remains a daily challenge due to the increasing number of cases and the lack of dermatologists. Thus, AI-assisted diagnosis is considered as a possible solution for this issue. Despite the great advances brought by deep learning and especially convolutional neural networks (CNNs), computer-aided diagnosis (CAD) systems are still not used in clinical practice. This may be explained by the dermatologist's fear of being misled by a false negative and the assimilation of CNNs to a "black box", making their decision process difficult to understand by a non-expert. Decision theory, especially game theory, is a potential solution as it focuses on identifying the best decision option that maximizes the decision-maker's expected utility. This study presents a new framework for automated melanoma diagnosis. Pursuing the goal of improving the performance of existing systems, our approach also attempts to bring more transparency in the decision process. The proposed framework includes a multi-class CNN and six binary CNNs assimilated to players. The players' strategies is to first cluster the pigmented lesions (melanoma, nevus, and benign keratosis), using the introduced method of evaluating the confidence of the predictions, into confidence level (confident, medium, uncertain). Then, a subset of players has the strategy to refine the diagnosis for difficult lesions with medium and uncertain prediction. We used EfficientNetB5 as the backbone of our networks and evaluated our approach on the public ISIC dataset consisting of 8917 lesions: melanoma (1113), nevi (6705) and benign keratosis (1099). The proposed framework achieved an area under the receiver operating curve (AUROC) of 0.93 for melanoma, 0.96 for nevus and 0.97 for benign keratosis. Furthermore, our approach outperformed existing methods in this task, improving the balanced accuracy (BACC) of the best compared method from 77% to 86%. These results suggest that our framework provides an effective and explainable decision-making strategy. This approach could help dermatologists in their clinical practice for patients with atypical and difficult-to-diagnose pigmented lesions. We also believe that our system could serve as a didactic tool for less experienced dermatologists.

Ensemble Method of Convolutional Neural Networks with Directed Acyclic Graph Using Dermoscopic Images: Melanoma Detection Application.

The early detection of melanoma is the most efficient way to reduce its mortality rate. Dermatologists achieve this task with the help of dermoscopy, a non-invasive tool allowing the visualization of patterns of skin lesions. Computer-aided diagnosis (CAD) systems developed on dermoscopic images are needed to assist dermatologists. These systems rely mainly on multiclass classification approaches. However, the multiclass classification of skin lesions by an automated system remains a challenging task. Decomposing a multiclass problem into a binary problem can reduce the complexity of the initial problem and increase the overall performance. This paper proposes a CAD system to classify dermoscopic images into three diagnosis classes: melanoma, nevi, and seborrheic keratosis. We introduce a novel ensemble scheme of convolutional neural networks (CNNs), inspired by decomposition and ensemble methods, to improve the performance of the CAD system. Unlike conventional ensemble methods, we use a directed acyclic graph to aggregate binary CNNs for the melanoma detection task. On the ISIC 2018 public dataset, our method achieves the best balanced accuracy (76.6%) among multiclass CNNs, an ensemble of multiclass CNNs with classical aggregation methods, and other related works. Our results reveal that the directed acyclic graph is a meaningful approach to develop a reliable and robust automated diagnosis system for the multiclass classification of dermoscopic images.

Spatial Location in Integrated Circuits through Infrared Microscopy.

In this paper, we present an infrared microscopy based approach for structures' location in integrated circuits, to automate their secure characterization. The use of an infrared sensor is the key device for internal integrated circuit inspection. Two main issues are addressed. The first concerns the scan of integrated circuits using a motorized optical system composed of an infrared uncooled camera combined with an optical microscope. An automated system is required to focus the conductive tracks under the silicon layer. It is solved by an autofocus system analyzing the infrared images through a discrete polynomial image transform which allows an accurate features detection to build a focus metric robust against specific image degradation inherent to the acquisition context. The second issue concerns the location of structures to be characterized on the conductive tracks. Dealing with a large amount of redundancy and noise, a graph-matching method is presented-discriminating graph labels are developed to overcome the redundancy, while a flexible assignment optimizer solves the inexact matching arising from noises on graphs. The resulting automated location system brings reproducibility for secure characterization of integrated systems, besides accuracy and time speed increase.

Fast Visual Odometry for a Low-Cost Underwater Embedded Stereo System †.

This paper provides details of hardware and software conception and realization of a stereo embedded system for underwater imaging. The system provides several functions that facilitate underwater surveys and run smoothly in real-time. A first post-image acquisition module provides direct visual feedback on the quality of the taken images which helps appropriate actions to be taken regarding movement speed and lighting conditions. Our main contribution is a light visual odometry method adapted to the underwater context. The proposed method uses the captured stereo image stream to provide real-time navigation and a site coverage map which is necessary to conduct a complete underwater survey. The visual odometry uses a stochastic pose representation and semi-global optimization approach to handle large sites and provides long-term autonomy, whereas a novel stereo matching approach adapted to underwater imaging and system attached lighting allows fast processing and suitability to low computational resource systems. The system is tested in a real context and shows its robustness and promising future potential.

Underwater Photogrammetry and Object Modeling: A Case Study of Xlendi Wreck in Malta.

In this paper we present a photogrammetry-based approach for deep-sea underwater surveys conducted from a submarine and guided by knowledge-representation combined with a logical approach (ontology). Two major issues are discussed in this paper. The first concerns deep-sea surveys using photogrammetry from a submarine. Here the goal was to obtain a set of images that completely covered the selected site. Subsequently and based on these images, a low-resolution 3D model is obtained in real-time, followed by a very high-resolution model produced back in the laboratory. The second issue involves the extraction of known artefacts present on the site. This aspect of the research is based on an a priori representation of the knowledge involved using systematic reasoning. Two parallel processes were developed to represent the photogrammetric process used for surveying as well as for identifying archaeological artefacts visible on the sea floor. Mapping involved the use of the CIDOC-CRM system (International Committee for Documentation (CIDOC)-Conceptual Reference Model)-This is a system that has been previously utilised to in the heritage sector and is largely available to the established scientific community. The proposed theoretical representation is based on procedural attachment; moreover, a strong link is maintained between the ontological description of the modelled concepts and the Java programming language which permitted 3D structure estimation and modelling based on a set of oriented images. A very recently discovered shipwreck acted as a testing ground for this project; the Xelendi Phoenician shipwreck, found off the Maltese coast, is probably the oldest known shipwreck in the western Mediterranean. The approach presented in this paper was developed in the scope of the GROPLAN project (Généralisation du Relevé, avec Ontologies et Photogrammétrie, pour l'Archéologie Navale et Sous-marine). Financed by the French National Research Agency (ANR) for four years, this project associates two French research laboratories, an industrial partner, the University of Malta, and Texas A & M University.