{"id":37065543,"url":"https://github.com/jb-sharp/medialaxis3d","last_synced_at":"2026-01-14T07:40:27.262Z","repository":{"id":307699063,"uuid":"1030420102","full_name":"jb-sharp/medialaxis3d","owner":"jb-sharp","description":"Python implementation of 3D Medial Axis Transform for 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returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["3d","mat","skeletonization"],"created_at":"2026-01-14T07:40:26.542Z","updated_at":"2026-01-14T07:40:27.250Z","avatar_url":"https://github.com/jb-sharp.png","language":"Cython","readme":"# medialaxis3d\n\nThis package extends the [scikit-image](https://scikit-image.org/) function [medial_axis](https://scikit-image.org/docs/stable/api/skimage.morphology.html#skimage.morphology.medial_axis)\nto the 3D case.\n\n## Install\n\n```bash\npip install medialaxis3d\n```\n\n### Dependencies\nAutomatically installed with `pip`:\n\n- `numpy`\n- `scipy`\n- `cython`\n\nOptional only for visualization\n\n- `napari`\n\n## Documentation \n\nWIP\n\n## Quickstart\n\nUse it without returning the medial distance.\n\n```Python\n\u003e\u003e\u003e import numpy as np\n\u003e\u003e\u003e import skimage as ski\n\u003e\u003e\u003e import medialaxis3d\n\u003e\u003e\u003e import napari\n\n\u003e\u003e\u003e rng = np.random.default_rng(1278)\n\n\u003e\u003e\u003e image = ski.data.binary_blobs(length = 128,\n\u003e\u003e\u003e                           blob_size_fraction = 0.2,\n\u003e\u003e\u003e                           n_dim = 3,\n\u003e\u003e\u003e                           volume_fraction = 0.6,\n\u003e\u003e\u003e                           rng = rng)\n\n\u003e\u003e\u003e skeleton = medialaxis3d.medial_axis_3d(image, \n\u003e\u003e\u003e                                        return_distance = False, \n\u003e\u003e\u003e                                        size = 8, \n\u003e\u003e\u003e                                        rng = rng)\n\n\u003e\u003e\u003e viewer = napari.Viewer()\n\u003e\u003e\u003e viewer.add_image(image, \n\u003e\u003e\u003e                  rendering = \"attenuated_mip\", \n\u003e\u003e\u003e                  attenuation = 0.5, \n\u003e\u003e\u003e                  scale = [1, 1, 1])\n\u003e\u003e\u003e viewer.add_image(skeleton, \n\u003e\u003e\u003e                  interpolation3d = \"nearest\", \n\u003e\u003e\u003e                  colormap = \"magenta\", \n\u003e\u003e\u003e                  scale = [1, 1, 1])\n\u003e\u003e\u003e napari.run()\n```\n\n\u003cimg src=\"https://raw.githubusercontent.com/jb-sharp/medialaxis3d/main/screenshots/example_nodist1.png\" width=\"32%\"/\u003e \u003cimg src=\"https://raw.githubusercontent.com/jb-sharp/medialaxis3d/main/screenshots/example_nodist2.png\" width=\"32%\"/\u003e \u003cimg src=\"https://raw.githubusercontent.com/jb-sharp/medialaxis3d/main/screenshots/example_nodist3.png\" width=\"32%\"/\u003e\n\nor use it to return the distance as well.\n\n```Python\n\u003e\u003e\u003e import numpy as np\n\u003e\u003e\u003e import skimage as ski\n\u003e\u003e\u003e import medialaxis3d\n\u003e\u003e\u003e import napari\n\n\u003e\u003e\u003e rng = np.random.default_rng(1278)\n\u003e\u003e\u003e image = ski.data.binary_blobs(length = 128,\n                              blob_size_fraction = 0.2,\n                              n_dim = 3,\n                              volume_fraction = 0.6,\n                              rng = rng)\n\n\u003e\u003e\u003e skeleton, distance = medialaxis3d.medial_axis_3d(image, \n\u003e\u003e\u003e                                                  return_distance = True, \n\u003e\u003e\u003e                                                  size = 8, \n\u003e\u003e\u003e                                                  rng = rng)\n\n\u003e\u003e\u003e viewer = napari.Viewer()\n\u003e\u003e\u003e viewer.add_image(image, \n\u003e\u003e\u003e                  rendering = \"attenuated_mip\", \n\u003e\u003e\u003e                  attenuation = 0.5, \n\u003e\u003e\u003e                  scale = [1, 1, 1])\n\u003e\u003e\u003e viewer.add_image(skeleton*distance, \n\u003e\u003e\u003e                  interpolation3d = \"nearest\", \n\u003e\u003e\u003e                  colormap = \"turbo\", \n\u003e\u003e\u003e                  scale = [1, 1, 1])\n\u003e\u003e\u003e napari.run()\n```\n\n\u003cimg src=\"https://raw.githubusercontent.com/jb-sharp/medialaxis3d/main/screenshots/example_nodist1.png\" width=\"32%\"/\u003e \u003cimg src=\"https://raw.githubusercontent.com/jb-sharp/medialaxis3d/main/screenshots/example_dist2.png\" width=\"32%\"/\u003e \u003cimg src=\"https://raw.githubusercontent.com/jb-sharp/medialaxis3d/main/screenshots/example_dist3.png\" width=\"32%\"/\u003e\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjb-sharp%2Fmedialaxis3d","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjb-sharp%2Fmedialaxis3d","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjb-sharp%2Fmedialaxis3d/lists"}