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Add to EdgeNazanin Moradinasab
Label-efficient Contrastive Learning-based model for nuclei detection and classification in 3D Cardiovascular Immunofluorescent Images
Sep 08, 2023
Recently, deep learning-based methods achieved promising performance in nuclei detection and classification applications. However, training deep learning-based methods requires a large amount of pixel-wise annotated data, which is time-consuming and labor-intensive, especially in 3D images. An alternative approach is to adapt weak-annotation methods, such as labeling each nucleus with a point, but this method does not extend from 2D histopathology images (for which it was originally developed) to 3D immunofluorescent images. The reason is that 3D images contain multiple channels (z-axis) for nuclei and different markers separately, which makes training using point annotations difficult. To address this challenge, we propose the Label-efficient Contrastive learning-based (LECL) model to detect and classify various types of nuclei in 3D immunofluorescent images. Previous methods use Maximum Intensity Projection (MIP) to convert immunofluorescent images with multiple slices to 2D images, which can cause signals from different z-stacks to falsely appear associated with each other. To overcome this, we devised an Extended Maximum Intensity Projection (EMIP) approach that addresses issues using MIP. Furthermore, we performed a Supervised Contrastive Learning (SCL) approach for weakly supervised settings. We conducted experiments on cardiovascular datasets and found that our proposed framework is effective and efficient in detecting and classifying various types of nuclei in 3D immunofluorescent images.
Weakly Supervised Deep Instance Nuclei Detection using Points Annotation in 3D Cardiovascular Immunofluorescent Images
Jul 29, 2022
Two major causes of death in the United States and worldwide are stroke and myocardial infarction. The underlying cause of both is thrombi released from ruptured or eroded unstable atherosclerotic plaques that occlude vessels in the heart (myocardial infarction) or the brain (stroke). Clinical studies show that plaque composition plays a more important role than lesion size in plaque rupture or erosion events. To determine the plaque composition, various cell types in 3D cardiovascular immunofluorescent images of plaque lesions are counted. However, counting these cells manually is expensive, time-consuming, and prone to human error. These challenges of manual counting motivate the need for an automated approach to localize and count the cells in images. The purpose of this study is to develop an automatic approach to accurately detect and count cells in 3D immunofluorescent images with minimal annotation effort. In this study, we used a weakly supervised learning approach to train the HoVer-Net segmentation model using point annotations to detect nuclei in fluorescent images. The advantage of using point annotations is that they require less effort as opposed to pixel-wise annotation. To train the HoVer-Net model using point annotations, we adopted a popularly used cluster labeling approach to transform point annotations into accurate binary masks of cell nuclei. Traditionally, these approaches have generated binary masks from point annotations, leaving a region around the object unlabeled (which is typically ignored during model training). However, these areas may contain important information that helps determine the boundary between cells. Therefore, we used the entropy minimization loss function in these areas to encourage the model to output more confident predictions on the unlabeled areas. Our comparison studies indicate that the HoVer-Net model trained using our weakly ...
Universal Hysteresis Identification Using Extended Preisach Neural Network
Dec 22, 2019
Hysteresis phenomena have been observed in different branches of physics and engineering sciences. Therefore, several models have been proposed for hysteresis simulation in different fields; however, almost neither of them can be utilized universally. In this paper by inspiring of Preisach Neural Network which was inspired by the Preisach model that basically stemmed from Madelungs rules and using the learning capability of the neural networks, an adaptive universal model for hysteresis is introduced and called Extended Preisach Neural Network Model. It is comprised of input, output and, two hidden layers. The input and output layers contain linear neurons while the first hidden layer incorporates neurons called Deteriorating Stop neurons, which their activation function follows Deteriorating Stop operator. Deteriorating Stop operators can generate non-congruent hysteresis loops. The second hidden layer includes Sigmoidal neurons. Adding the second hidden layer, helps the neural network learn non-Masing and asymmetric hysteresis loops very smoothly. At the input layer, besides input data the rate at which input data changes, is included as well in order to give the model the capability of learning rate-dependent hysteresis loops. Hence, the proposed approach has the capability of the simulation of both rate-independent and rate-dependent hysteresis with either congruent or non-congruent loops as well as symmetric and asymmetric loops. A new hybridized algorithm has been adopted for training the model which is based on a combination of the Genetic Algorithm and the optimization method of sub-gradient with space dilatation. The generality of the proposed model has been evaluated by applying it to various hysteresis from different areas of engineering with different characteristics. The results show that the model is successful in the identification of the considered hystereses.