Neural tissue grower

This page describes software for generating connectivity volumes. The aim is to generate artificial EM-level volume data for testing algorithms for performing automated reconstruction of connectivity.

This picture shows a raytraced version of the connectivity.

After generating the initial connectivity, an update algorithm forms clumps.

This picture is a short animation - reload to see it again.

The growth process starts by expanding the dendrite. The dendrite is represented by a line of overlapping spheres, whose radius reduces at branches.

The dendrite branches according to the algorithm parameters. These include the probability of branching, the number of children at a branch, and the maximum size.

This growth rule leaves gaps and can produce overlaps. After the initial growth phase, an algorithm iteratively applies forces to the dendrites as follows:

• A strong repulsive force to stop overlaps
• A strong attractive force to stop dendrites from splitting apart
• A weak attractive force between dendrites from different cells to reduce free space.

Fred Howell, ANC, Informatics, University of Edinburgh