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 quantification method capable of automatically quantifying neuronal morphologies such as soma number and size, neurite length, and neurite branching complexity (which is highly related to the numbers of attachment points and ending points). NeurphologyJ is implemented as a plugin to ImageJ, an open-source Java-based image processing and analysis platform.
An interactive 3D axon tracking and labeling tool to obtain quantitative information by reconstruction of the axonal structures in the entire innervation field. AxonTracker-3D has been developed to facilitate the connectome function analysis in large-scale quantitative neurobiology studies. It can display the three orthogonal views of the current location of the centerline along with a visualization of the tracking results. The workflow consists of three steps: (i) re-slice the axon tubes along its orientation; (ii) extract 2D and 3D features from the slices and spheres rounding the center points; (iii) select samples to train AdaBoost classifier. Questions such as whether the spatial distribution of the axons are random in nature or follow a certain pattern can be answered with this tool.
A statistical method for tracing the branch centerlines of neurons based on Bayesian multi-object tracking using probability hypothesis density (PHD) filtering. hgpush is able to simultaneously trace out multiple neuron structures in a probabilistic fashion so that the same neuron segments may be covered multiple times and are thus supported by more evidence. The main novelty is that it combines the problems of neuron segment detection and linking into one framework by performing simultaneous multi-object tracking. hgpush solves the computational problems of direct Bayesian multi-object tracking and allows convenient handling of bifurcations and terminations during the tracing process by modeling of spawned objects and observation clutter.
Allows to track populations of neurons with single neuron resolution in the brain of a freely moving C. elegans undergoing large motion and deformation. NeRVEclustering uses non-rigid point-set registration in order to match each segmented neuron in each volume with a set of reference volumes taken from throughout the recording. This tool primarily serves for tracking neurons in brains undergoing large deformations.
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