About

pcg_skel is a package used to rapidly build neuronal skeletons from electron microscopy data in the CAVE ecosystem. It integrates structural data, connectivity data, and local features stored across many aspects of a CAVE system, and creates objects as MeshParty meshes, skeletons, and MeshWork files for subsequent analysis. By harnessing the way the structural data is stored, you can build skeletons for even very large neurons quickly and with little memory use.

Installation¶

To install pcg_skel, just use pip. The package is available for python 3.9 and above.

pip install pcg_skel

Installing from Source (for Developers)¶

To install pcg_skel from source, you can clone the repository and install it using pip.

pip install -e .

pcg_skel uses Hatch for packaging, and there are tests that can be run within the environment using:

hatch run test:run_tests

MeshParty¶

pcg_skel uses MeshParty for skeletonization and mesh processing, and relies on algorithms and data classes defined there.

CAVEclient¶

pcg_skel uses the CAVEclient to access data stored in the CAVE ecosystem.

SkeletonPlot¶

SkeletonPlot can be used to visualize skeletons generated by pcg_skel.