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Voxel filler

This page describes an program for reconstructing neurons from membrane outlines. It uses a fast marching algorithm, a 3D extension of the one in: 2D fast marching.. The test data comes from a 3D neuron tissue grower.

This picture shows the starting point - a 3D volume of membranes.

This picture shows the fill in progress. Two overlapping branched dendrites are being filled in green. The magenta colour shows the boundary of the filled region; the membrane is in white.

A slice through the voxel stack.

Filling in progress. Note that many neurons can be filled at the same time - and that in a single slice, it is hard to determine which fragments of dendrites belong to which neuron.

After filling has reached a certain stage, the different neurons can be coloured using a quick flood fill to find contiguous voxel regions.

The algorithm works by:

It gains over a simple "flood fill" as it expands at the global minimum of the boundary of the already filled area - making it less likely to breach cell boundaries if there is more cell to fill.

Some of the problems for the algorithm: