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Comparative analysis of metabolic models of microbial communities reconstructed from automated tools and consensus approaches
Genome-scale metabolic models (GEMs) of microbial communities offer valuable insights into the functional capabilities of their members and...
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RoboEM: automated 3D flight tracing for synaptic-resolution connectomics
Map** neuronal networks from three-dimensional electron microscopy (3D-EM) data still poses substantial reconstruction challenges, in particular...
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Automated synapse-level reconstruction of neural circuits in the larval zebrafish brain
Dense reconstruction of synaptic connectivity requires high-resolution electron microscopy images of entire brains and tools to efficiently trace...
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BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets
BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We...
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Automated Cryo Electron Tomography Data Collection
Electron tomography entails the three-dimensional reconstruction of an object from its projections, which are acquired using a transmission electron...
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Automated high-speed 3D imaging of organoid cultures with multi-scale phenotypic quantification
Current imaging approaches limit the ability to perform multi-scale characterization of three-dimensional (3D) organotypic cultures (organoids) in...
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DRPnet: automated particle picking in cryo-electron micrographs using deep regression
BackgroundIdentification and selection of protein particles in cryo-electron micrographs is an important step in single particle analysis. In this...
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Automated Segmentation and 3D Reconstruction of Different Membranes from Confocal Z-Stacks
Confocal laser scanning microscopy (CLSM) is an advanced microscopy technique based on fluorescence technology which produces sharp images of a...
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PAReTT: A Python Package for the Automated Retrieval and Management of Divergence Time Data from the TimeTree Resource for Downstream Analyses
Evolutionary processes happen gradually over time and are, thus, considered time dependent. In addition, several evolutionary processes are either...
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Underestimation of the Effect of Biologiocal Invasions in Phylogeographic Reconstructions as Seen in Daphnia magna (Crustacea, Cladocera)
Abstract —A phylogeographic analysis of Daphnia magna Straus 1820 (Crustacea, Cladocera) was used to study the consequences of underestimating the...
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Data-driven regularization lowers the size barrier of cryo-EM structure determination
Macromolecular structure determination by electron cryo-microscopy (cryo-EM) is limited by the alignment of noisy images of individual particles....
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FlyWire: online community for whole-brain connectomics
Due to advances in automated image acquisition and analysis, whole-brain connectomes with 100,000 or more neurons are on the horizon. Proofreading of...
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Cryo-Electron Microscopy at the Biological Faculty of Moscow State University
AbstractThe paper reports an example of a successful upgrade of the JEOL JEM-2100 analytical transmission electron microscope to a low-resolution...
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DeepACSON automated segmentation of white matter in 3D electron microscopy
Tracing the entirety of ultrastructures in large three-dimensional electron microscopy (3D-EM) images of the brain tissue requires automated...
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Automated reconstruction of whole-embryo cell lineages by learning from sparse annotations
We present a method to automatically identify and track nuclei in time-lapse microscopy recordings of entire develo** embryos. The method combines...
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Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine
The human microbiome influences the efficacy and safety of a wide variety of commonly prescribed drugs. Designing precision medicine approaches that...
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Volumetric 3D reconstruction of plant leaf cells using SEM, ion milling, TEM, and serial sectioning
Main conclusionFocused ion beam scanning electron microscopy is well suited for volumetric extractions and 3D reconstructions of plant cells and its...
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Automated generation of genome-scale metabolic draft reconstructions based on KEGG
BackgroundConstraint-based modeling is a widely used and powerful methodology to assess the metabolic phenotypes and capabilities of an organism. The...
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Detailed map** of the complex fiber structure and white matter pathways of the chimpanzee brain
Long-standing questions about human brain evolution may only be resolved through comparisons with close living evolutionary relatives, such as...
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Testing Phylogenetic Stability with Variable Taxon Sampling
Over the past three decades, computational capabilities have grown at such a rapid rate that they have given rise to many computationally heavy...