Deep convolutional neural networks for segmenting 3D in vivo multiphoton images of vasculature in Alzheimer disease mouse models

The health and function of tissue rely on its vasculature network to provide reliable blood perfusion. Volumetric imaging approaches, such as multiphoton microscopy, are able to generate detailed 3D images of blood vessels that could contribute to our understanding of the role of vascular structure in normal physiology and in disease mechanisms. The segmentation of vessels, a core image analysis problem, is a bottleneck that has prevented the systematic comparison of 3D vascular architecture across experimental populations. We explored the use of convolutional neural networks to segment 3D vessels within volumetric in vivo images acquired by multiphoton microscopy. We evaluated different network architectures and machine learning techniques in the context of this segmentation problem. We show that our optimized convolutional neural network architecture, which we call DeepVess, yielded a segmentation accuracy that was better than both the current state-of-the-art and a trained human annotator, while also being orders of magnitude faster. To explore the effects of aging and Alzheimer's disease on capillaries, we applied DeepVess to 3D images of cortical blood vessels in young and old mouse models of Alzheimer's disease and wild type littermates. We found little difference in the distribution of capillary diameter or tortuosity between these groups, but did note a decrease in the number of longer capillary segments ($>75\mu m$) in aged animals as compared to young, in both wild type and Alzheimer's disease mouse models.Comment: 34 pages, 9 figure

Highly accurate detection of ovarian cancer using CA125 but limited improvement with serum matrix-assisted laser desorption/ionization time-of-flight mass spectrometry profiling

Objectives: Our objective was to test the performance of CA125 in classifying serum samples from a cohort of malignant and benign ovarian cancers and age-matched healthy controls and to assess whether combining information from matrix-assisted laser desorption/ionization (MALDI) time-of-flight profiling could improve diagnostic performance. Materials and Methods: Serum samples from women with ovarian neoplasms and healthy volunteers were subjected to CA125 assay and MALDI time-of-flight mass spectrometry (MS) profiling. Models were built from training data sets using discriminatory MALDI MS peaks in combination with CA125 values and tested their ability to classify blinded test samples. These were compared with models using CA125 threshold levels from 193 patients with ovarian cancer, 290 with benign neoplasm, and 2236 postmenopausal healthy controls. Results: Using a CA125 cutoff of 30 U/mL, an overall sensitivity of 94.8% (96.6% specificity) was obtained when comparing malignancies versus healthy postmenopausal controls, whereas a cutoff of 65 U/mL provided a sensitivity of 83.9% (99.6% specificity). High classification accuracies were obtained for early-stage cancers (93.5% sensitivity). Reasons for high accuracies include recruitment bias, restriction to postmenopausal women, and inclusion of only primary invasive epithelial ovarian cancer cases. The combination of MS profiling information with CA125 did not significantly improve the specificity/accuracy compared with classifications on the basis of CA125 alone. Conclusions: We report unexpectedly good performance of serum CA125 using threshold classification in discriminating healthy controls and women with benign masses from those with invasive ovarian cancer. This highlights the dependence of diagnostic tests on the characteristics of the study population and the crucial need for authors to provide sufficient relevant details to allow comparison. Our study also shows that MS profiling information adds little to diagnostic accuracy. This finding is in contrast with other reports and shows the limitations of serum MS profiling for biomarker discovery and as a diagnostic too

CASM-AMFMNet: A Network based on Coordinate Attention Shuffle Mechanism and Asymmetric Multi-Scale Fusion Module for Classification of Grape Leaf Diseases

Grape disease is a significant contributory factor to the decline in grape yield, typically affecting the leaves first. Efficient identification of grape leaf diseases remains a critical unmet need. To mitigate background interference in grape leaf feature extraction and improve the ability to extract small disease spots, by combining the characteristic features of grape leaf diseases, we developed a novel method for disease recognition and classification in this study. First, Gaussian filters Sobel smooth de-noising Laplace operator (GSSL) was employed to reduce image noise and enhance the texture of grape leaves. A novel network designated coordinated attention shuffle mechanism-asymmetric multi-scale fusion module net (CASM-AMFMNet) was subsequently applied for grape leaf disease identification. CoAtNet was employed as the network backbone to improve model learning and generalization capabilities, which alleviated the problem of gradient explosion to a certain extent. The CASM-AMFMNet was further utilized to capture and target grape leaf disease areas, therefore reducing background interference. Finally, Asymmetric multi-scale fusion module (AMFM) was employed to extract multi-scale features from small disease spots on grape leaves for accurate identification of small target diseases. The experimental results based on our self-made grape leaf image dataset showed that, compared to existing methods, CASM-AMFMNet achieved an accuracy of 95.95%, F1 score of 95.78%, and mAP of 90.27%. Overall, the model and methods proposed in this report could successfully identify different diseases of grape leaves and provide a feasible scheme for deep learning to correctly recognize grape diseases during agricultural production that may be used as a reference for other crops diseases

CASM-AMFMNet: A Network based on Coordinate Attention Shuffle Mechanism and Asymmetric Multi-Scale Fusion Module for Classification of Grape Leaf Diseases

Grape disease is a significant contributory factor to the decline in grape yield, typically affecting the leaves first. Efficient identification of grape leaf diseases remains a critical unmet need. To mitigate background interference in grape leaf feature extraction and improve the ability to extract small disease spots, by combining the characteristic features of grape leaf diseases, we developed a novel method for disease recognition and classification in this study. First, Gaussian filters Sobel smooth de-noising Laplace operator (GSSL) was employed to reduce image noise and enhance the texture of grape leaves. A novel network designated coordinated attention shuffle mechanism-asymmetric multi-scale fusion module net (CASM-AMFMNet) was subsequently applied for grape leaf disease identification. CoAtNet was employed as the network backbone to improve model learning and generalization capabilities, which alleviated the problem of gradient explosion to a certain extent. The CASM-AMFMNet was further utilized to capture and target grape leaf disease areas, therefore reducing background interference. Finally, Asymmetric multi-scale fusion module (AMFM) was employed to extract multi-scale features from small disease spots on grape leaves for accurate identification of small target diseases. The experimental results based on our self-made grape leaf image dataset showed that, compared to existing methods, CASM-AMFMNet achieved an accuracy of 95.95%, F1 score of 95.78%, and mAP of 90.27%. Overall, the model and methods proposed in this report could successfully identify different diseases of grape leaves and provide a feasible scheme for deep learning to correctly recognize grape diseases during agricultural production that may be used as a reference for other crops diseases