neurite tracing

All-path-pruning 2.0 (APP2) is a component of Vaa3D. APP2 prunes an initial reconstruction tree of a neuron’s morphology using a long-segment-first hierarchical procedure instead of the original termini-first-search process in APP. APP2 computes the distance transform of all image voxels directly for a gray-scale image, without the need to binarize the image before invoking the conventional distance transform. APP2 uses a fast-marching algorithm-based method to compute the initial reconstruction trees without pre-computing a large graph. This method allows to trace large images. This method can be used with default parameters or user-defined parameters.

"We have developed an automatic graph algorithm, called the all-path pruning (APP), to trace the 3D structure of a neuron. To avoid potential mis-tracing of some parts of a neuron, an APP first produces an initial over-reconstruction, by tracing the optimal geodesic shortest path from the seed location to every possible destination voxel/pixel location in the image. Since the initial reconstruction contains all the possible paths and thus could contain redundant structural components (SC), we simplify the entire reconstruction without compromising its connectedness by pruning the redundant structural elements, using a new maximal- covering minimal-redundant (MCMR) subgraph algorithm. We show that MCMR has a linear computational complexity and will converge. We examined the performance of our method using challenging 3D neuronal image datasets of model organisms (e.g. fruit fly)"

This plugin can be used with default parameters or user-defined parameters.

Deprecated component -- superseded by SNT. Legacy description follows:

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Plugin designed to allow easy semi-automatic tracing of neurons or other filament-like structures (e.g., microtubules, blood vessels) through either 2D images or 3D image stacks. Data can be imported and exported in SWC files for interaction with other software, or details of the traces can be exported as CSV files for analysis in spreadsheets or statistical software.

This plugin is included in Fiji by default.