Neuron tracing from light microscopy images: automation, deep learning and bench testing
Motivation Large-scale neuronal morphologies are essential to neuronal typing, connectivity
characterization and brain modeling. It is widely accepted that automation is critical to the …
characterization and brain modeling. It is widely accepted that automation is critical to the …
Automated neuron tracing methods: an updated account
L Acciai, P Soda, G Iannello - Neuroinformatics, 2016 - Springer
The reconstruction of neuron morphology allows to investigate how the brain works, which is
one of the foremost challenges in neuroscience. This process aims at extracting the …
one of the foremost challenges in neuroscience. This process aims at extracting the …
[HTML][HTML] NBLAST: rapid, sensitive comparison of neuronal structure and construction of neuron family databases
Neural circuit mapping is generating datasets of tens of thousands of labeled neurons. New
computational tools are needed to search and organize these data. We present NBLAST, a …
computational tools are needed to search and organize these data. We present NBLAST, a …
Whole-brain tissue mapping toolkit using large-scale highly multiplexed immunofluorescence imaging and deep neural networks
Mapping biological processes in brain tissues requires piecing together numerous
histological observations of multiple tissue samples. We present a direct method that …
histological observations of multiple tissue samples. We present a direct method that …
Brain capillary networks across species: a few simple organizational requirements are sufficient to reproduce both structure and function
Despite the key role of the capillaries in neurovascular function, a thorough characterization
of cerebral capillary network properties is currently lacking. Here, we define a range of …
of cerebral capillary network properties is currently lacking. Here, we define a range of …
SOAX: a software for quantification of 3D biopolymer networks
Filamentous biopolymer networks in cells and tissues are routinely imaged by confocal
microscopy. Image analysis methods enable quantitative study of the properties of these …
microscopy. Image analysis methods enable quantitative study of the properties of these …
A graph-theoretical approach for tracing filamentary structures in neuronal and retinal images
The aim of this study is about tracing filamentary structures in both neuronal and retinal
images. It is often crucial to identify single neurons in neuronal networks, or separate vessel …
images. It is often crucial to identify single neurons in neuronal networks, or separate vessel …
Reconstructing loopy curvilinear structures using integer programming
We propose a novel approach to automated delineation of linear structures that form
complex and potentially loopy networks. This is in contrast to earlier approaches that usually …
complex and potentially loopy networks. This is in contrast to earlier approaches that usually …
BlastNeuron for Automated Comparison, Retrieval and Clustering of 3D Neuron Morphologies
Characterizing the identity and types of neurons in the brain, as well as their associated
function, requires a means of quantifying and comparing 3D neuron morphology. Presently …
function, requires a means of quantifying and comparing 3D neuron morphology. Presently …
Scalable robust graph and feature extraction for arbitrary vessel networks in large volumetric datasets
D Drees, A Scherzinger, R Hägerling, F Kiefer… - BMC …, 2021 - Springer
Background Recent advances in 3D imaging technologies provide novel insights to
researchers and reveal finer and more detail of examined specimen, especially in the …
researchers and reveal finer and more detail of examined specimen, especially in the …