Skip to content

basic voxelization (segmentation) tool added

Pre-release
Pre-release
Compare
Choose a tag to compare
@jewettaij jewettaij released this 17 Dec 04:14
· 217 commits to master since this release

A python script (voxelize_mesh.py) has been added and documented which should finally make segmentation of membrane-bound compartments possible (if not easy). This tool generates an image which indicates which voxels lie within a closed surface mesh. Meshes corresponding to surfaces (eg. boundaries of cells or organelles) can be generated using a combination of "filter_mrc" with tensor-voting, together with PoissonRecon, and meshlab to close, smooth, and cleanup the resulting meshes. Although this tool only segments a single closed surface in the the image, multiple different segmentations can be combined into the same image (using the combine_mrc program) to create a true segmentation containing multiple different labelled objects.

(The resulting segmented images can be used as masks to help other feature detection programs, such as filter_mrc, restrict the search for features to relevant places. For example, a mask might help search for ribosomes inside a bacterial cell, not outside the cell.)

WARNING: voxelize_mesh.py is extremely inefficient

The voxelize_mesh.py script is very slow and it consumes an extremely large amount of memory due to the fact that it relies on 3rd-party code. (It is so inefficient that it is barely functional. But for now it is good enough for my own needs.) Please read the documentation for that program if you decide to attempt using it.