vianamp / shellexpansion

Segmentation algorithm based on region-growing

Region Growing Segmentation

File xx.info contains information about the z-stack and a list of seeds coordinates. For each seed, we grow a blob shell-by-shell as we monitore the number of connected components of the current shell. Only components larger than Smin pixels are allowed to grow. In addition, voxels of th current shell are allowed to recruit new voxels for the next shell only if their intensity is lower than threshold.

Parameters

• threshold: maximum internsity allowed for a voxel to be incorporated in the growing blob.

• Smin: Minimum number of voxels that a component of a shell has to have in order to grow.

Things to do and further improvements

The algorithm prevents the growing region from leaking in many circustances, but this requires the leakage to occurs as a disconnected component. If this is not the case, the algorithm will fail. Something else has to be done in those cases.

• Monitore the curvature of the growing region voxel-by-voxel and use it as another parameter to determine whether a given voxel can grow.

• Resample the resulting surface according to SpacingXY and SpacingZ specified info file.

• Implement a new method for generating seeds automatically.

How to run

./ShellExpansion -path PATH_TO_YOUR_INFO_FILE -smin 50 -threshold 15000

Matheus Palhares Viana 06.16.2016