Assists in automating and multithreading Sholl for direct analysis of fluorescent images and traced morphologies. Sholl analysis is a plugin for the image analysis software ImageJ. It creates a serie of concentric circles around the soma of the neuron, and counts how many times the neuron intersects with the circumference of these circles. This software can be applied universally to gray-scale images of neurons of different shapes or sizes.
A method for 2-d segmentation, classification and analysis of structural/plastic changes of hippocampal dendritic spines. A user interactive segmentation method with convolution kernels is designed to segment the spines from the dendrites. Formal morphological definitions are presented to describe key attributes related to the shape of segmented spines. Spines are automatically classified into one of four classes: Stubby, Filopodia, Mushroom and Spine-head Protrusions. 2dSpAn is a tool for fast and accurate annotation of dendritic spines from confocal microscopy images. However, the 2dSpAn method allows determining the morphology of spines from super-resolution microscopy and is not limited only to confocal images.
A pipeline for the reconstruction of discontinuous neuronal morphology in noisy images. SparseTracer is based on two methods. One is the region-to-region connection (RRC) method for detecting the initial part of a neurite, which can effectively gather local cues, i.e., avoid the whole image analysis, and thus boosts the efficacy of computation. The other is constrained principal curves method for completing the neurite reconstruction, which uses the past reconstruction information of a neurite for current reconstruction and thus can be suitable for tracing discontinuous neurites. SparseTracer is able to deal with the large-scale image dataset.
Allows users to reconstruct and proofread neuronal morphologies in light microscopy images. The system incorporates automatic tracing and manual editing of neuron reconstruction into a cooperative 3D interactive visualization-assisted environment, which is a powerful tool for analysis of complex neuronal images.
An automatic neuron tracing method. DF-Tracing can automatically trace complicated neuron structures set in noise-contaminated microscopic images. This method first extracts the neurite signal (foreground) from a noisy image by using anisotropic filtering and automated thresholding. Then, DF-Tracing executes a coupled distance-field (DF) algorithm on the extracted foreground neurite signal and reconstructs the neuron morphology automatically.
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