Here we surveyed bioinformatics software tools for quantifiy neurite extension and retraction from sequences of digital time-lapse series of images obtained by conventional fluorescence microscopy . Tools are ranked by the biomedical research community.
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 Java-based software tool designed for semi-automated quantification of neurite extension and retraction from sequences of digital time-lapse series of images. NeuronGrowth can be applied to image sequences acquired under phase contrast, differential interference contrast (DIC) and fluorescence optics.
Gives a reliable quantitative analysis of neurite growth, providing counts of neurite number and neurite area at different distances from the explant. Moreover, this plug-in follows lineal and semi-logarithmic analysis of the Sholl method, yielding a numerical value of neurite outgrowth useful for comparing different experimental conditions. Neurite-J provides a quantification method of neurite arbors in 3D organotypic cultures that gives the researcher an easy, fast and reliable tool to study axonal growth.
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