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.