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To build the connectomics map of the brain, we developed a new algorithm that can automatically refine the Membrane Detection Probability Maps (MDPM) generated to perform automatic segmentation of electron microscopy (EM) images. To achieve…
Automated and semi-automated techniques in biomedical electron microscopy (EM) enable the acquisition of large datasets at a high rate. Segmentation methods are therefore essential to analyze and interpret these large volumes of data, which…
The most established method of reconstructing neural circuits from animals involves slicing tissue very thin, then taking mosaics of electron microscope (EM) images. To trace neurons across different images and through different sections,…
Automated sample preparation and electron microscopy enables acquisition of very large image data sets. These technical advances are of special importance to the field of neuroanatomy, as 3D reconstructions of neuronal processes at the nm…
Biological membranes are one of the most basic structures and regions of interest in cell biology. In the study of membranes, segment extraction is a well-known and difficult problem because of impeding noise, directional and thickness…
Morphology of mitochondria plays critical roles in mediating their physiological functions. Accurate segmentation of mitochondria from 3D electron microscopy (EM) images is essential to quantitative characterization of their morphology at…
We present an interactive approach to train a deep neural network pixel classifier for the segmentation of neuronal structures. An interactive training scheme reduces the extremely tedious manual annotation task that is typically required…
Semantic segmentation is the task of classifying each pixel in an image. Training a segmentation model achieves best results using annotated images, where each pixel is annotated with the corresponding class. When obtaining fine annotations…
Semantic segmentation is a critical task in computer vision aiming to identify and classify individual pixels in an image, with numerous applications in for example autonomous driving and medical image analysis. However, semantic…
Pixel and superpixel classifiers have become essential tools for EM segmentation algorithms. Training these classifiers remains a major bottleneck primarily due to the requirement of completely annotating the dataset which is tedious,…
Region-based methods have proven necessary for improving segmentation accuracy of neuronal structures in electron microscopy (EM) images. Most region-based segmentation methods use a scoring function to determine region merging. Such…
Producing connectomes from electron microscopy (EM) images has historically required a great deal of human proofreading effort. This manual annotation cost is the current bottleneck in scaling EM connectomics, for example, in making larger…
Although deep encoder-decoder networks have achieved astonishing performance for mitochondria segmentation from electron microscopy (EM) images, they still produce coarse segmentations with lots of discontinuities and false positives.…
We aim to improve segmentation through the use of machine learning tools during region agglomeration. We propose an active learning approach for performing hierarchical agglomerative segmentation from superpixels. Our method combines…
Electron tomography (ET) allows high-resolution reconstructions of macromolecular complexes at nearnative state. Cellular structures segmentation in the reconstruction data from electron tomographic images is often required for analyzing…
Automatic segmentation of neuronal topology is critical for handling large scale neuroimaging data, as it can greatly accelerate neuron annotation and analysis. However, the intricate morphology of neuronal branches and the occlusions among…
Autoencoding, which aims to reconstruct the input images through a bottleneck latent representation, is one of the classic feature representation learning strategies. It has been shown effective as an auxiliary task for semi-supervised…
The alignment of serial-section electron microscopy (ssEM) images is critical for efforts in neuroscience that seek to reconstruct neuronal circuits. However, each ssEM plane contains densely packed structures that vary from one section to…
Deep convolutional neural networks have driven substantial advancements in the automatic understanding of images. Requiring a large collection of images and their associated annotations is one of the main bottlenecks limiting the adoption…
Cellular Electron Cryo-Tomography (CECT) is a powerful imaging technique for the 3D visualization of cellular structure and organization at submolecular resolution. It enables analyzing the native structures of macromolecular complexes and…