skeletonization

Reconstructed object skeletonization.
This repository is outdated. Please refer to https://github.com/seung-lab/kimimaro for skeletonization.

Skeletonization pipeline

Point cloud generation (object.py) >>> Skeletonization (skeletonize.py) >>> Post-process (postprocess.py)

Point cloud generation

object.py

Usage:

python3 object.py /segmentation/dir/ object_id mip_level /cell_info/json_file/dir/ /output_filename

python3 object.py gs://neuroglancer/pinky40_v11/watershed_mst_trimmed_sem_remap/ 20763362 3 g
s://neuroglancer/pinky40_v11/watershed_mst_trimmed_sem_remap/mesh_mip_3_err_40/ ./test.npy`

from object import *

extract_points_object('/segmentation/dir/', object_id, mip_level, '/cell_info/json_file', '/output_filename')