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Single cell segmentation is critical and challenging in live cell imaging data analysis. Traditional image processing methods and tools require time-consuming and labor-intensive efforts of manually fine-tuning parameters. Slight variations…
We propose a cell segmentation method for analyzing images of densely clustered cells. The method combines the strengths of marker-controlled watershed transformation and a convolutional neural network (CNN). We demonstrate the method…
We consider the problem of accurately identifying cell boundaries and labeling individual cells in confocal microscopy images, specifically, 3D image stacks of cells with tagged cell membranes. Precise identification of cell boundaries,…
Automated segmentation approaches are crucial to quantitatively analyze large-scale 3D microscopy images. Particularly in deep tissue regions, automatic methods still fail to provide error-free segmentations. To improve the segmentation…
Imaging assays of cellular function, especially those using fluorescent stains, are ubiquitous in the biological and medical sciences. Despite advances in computer vision, such images are often analyzed using only manual or rudimentary…
We propose a dual pathway, 11-layers deep, three-dimensional Convolutional Neural Network for the challenging task of brain lesion segmentation. The devised architecture is the result of an in-depth analysis of the limitations of current…
There is an increasing interest in applying deep learning to 3D mesh segmentation. We observe that 1) existing feature-based techniques are often slow or sensitive to feature resizing, 2) there are minimal comparative studies and 3)…
Object segmentation and structure localization are important steps in automated image analysis pipelines for microscopy images. We present a convolution neural network (CNN) based deep learning architecture for segmentation of objects in…
Deep convolutional neural networks (CNNs) have been intensively used for multi-class segmentation of data from different modalities and achieved state-of-the-art performances. However, a common problem when dealing with large, high…
The ability to automatically detect certain types of cells or cellular subunits in microscopy images is of significant interest to a wide range of biomedical research and clinical practices. Cell detection methods have evolved from…
Volumetric cell segmentation in fluorescence microscopy images is important to study a wide variety of cellular processes. Applications range from the analysis of cancer cells to behavioral studies of cells in the embryonic stage. Like in…
Fluorescence microscopy is an essential tool for the analysis of 3D subcellular structures in tissue. An important step in the characterization of tissue involves nuclei segmentation. In this paper, a two-stage method for segmentation of…
We propose a 3D convolutional neural network to simultaneously segment and detect cell nuclei in confocal microscopy images. Mirroring the co-dependency of these tasks, our proposed model consists of two serial components: the first part…
Tracking cells in 3D at high speed continues to attract extensive attention for many biomedical applications, such as monitoring immune cell migration and observing tumor metastasis in flowing blood vessels. Here, we propose a deep…
Multi-organ segmentation is one of most successful applications of deep learning in medical image analysis. Deep convolutional neural nets (CNNs) have shown great promise in achieving clinically applicable image segmentation performance on…
We present an efficient deep learning approach for the challenging task of tumor segmentation in multisequence MR images. In recent years, Convolutional Neural Networks (CNN) have achieved state-of-the-art performances in a large variety of…
We introduce a method to classify imagery using a convo- lutional neural network (CNN) on multi-view image pro- jections. The power of our method comes from using pro- jections of multiple images at multiple depth planes near the…
The presented algorithms for segmentation and tracking follow a 3-step approach where we detect, track and finally segment nuclei. In the preprocessing phase, we detect centroids of the cell nuclei using a convolutional neural network (CNN)…
Recently, the concept of unsupervised learning for superpixel segmentation via CNNs has been studied. Essentially, such methods generate superpixels by convolutional neural network (CNN) employed on a single image, and such CNNs are trained…
State-of-the-art image segmentation algorithms generally consist of at least two successive and distinct computations: a boundary detection process that uses local image information to classify image locations as boundaries between objects,…