osteoid

Skeleton object used for representing neurons, adjacent cells, and organelles.

Osteoid is the Skeleton code from CloudVolume refactored into its own library.

Installation

pip install osteoid

Examples

import osteoid

skel = osteoid.load("skeleton.swc")
osteoid.save("skeleton.swc", skel)

from osteoid import Skeleton, Bbox

skel = Skeleton(vertices, edges, radii=radii)

# you can specify a transform to e.g.
# convert the skeleton into a physical space
# with, in this example, 16x16x40 nm^3 resolution

matrix = np.array([
  [16, 0, 0, 0],
  [0, 16, 0, 0],
  [0, 0, 40, 0],
], dtype=np.float32)

skel = Skeleton(vertices, edges, radii=radii, transform=matrix)
skel = skel.physical_space() # applies transform to vertices
skel = skel.voxel_space() # removes transform from vertices

# skeleton functions

l = skel.cable_length() # physical length of the cable
comps = skel.components() # connected components
paths = skel.paths() # convert tree into a list of linear paths
skel = skel.downsample(factor) # factor must be a pos integer
skel = skel.average_smoothing(7) # smooths over a window of e.g. 7 vertices

skel2 = skel.crop([ minx, miny, minz, maxx, maxy, maxz ])
skel2 = skel.crop(Bbox([minx, miny, minz], [maxx, maxy, maxz]))

G = skel.to_networkx() # converts edges to an nx.Graph()

binary = skel.to_precomputed() # Neuroglancer compatible format
swc = skel.to_swc() # Neuroglancer compatible format
skel = Skeleton.from_swc(swc)
skel = Skeleton.from_precomputed(binary, segid=1, vertex_attributes=[
      {
        'id': 'radius',
        'num_components': 1,
        'data_type': 'float32',
      },
])

# Cross-format transform from Navis. More efficient than 
# using SWCs as an interchange medium. Navis is more fully featured,
# and written with a lot of love by Philipp Schlegel and others.
# Consider using it and citing them: https://github.com/navis-org/navis
skel = Skeleton.from_navis(navis_skel)

# remove duplicate vertices and optionally disconnected vertices
skel = skel.consolidate() 
skel2 = skel.clone()

# visualize, requires either matplotlib or microviewer+vtk installed
skel.viewer() # select library automatically

skel.viewer(color_by='radius', library='matplotlib')
skel.viewer(color_by='cross_section', library='matplotlib')
skel.viewer(color_by='component', library='matplotlib')

# gpu accelerated, fewer features, colors by component
skel.viewer(library='vtk')

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Latest release

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for willsilversmith from gravatar.com willsilversmith

Credits

Author: William Silversmith

License

BSD-3 Clause

Requires

Python >=3.9

Report project as malware

Metadata

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Latest release

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for willsilversmith from gravatar.com willsilversmith

Credits

Author: William Silversmith

License

BSD-3 Clause

Requires

Python >=3.9

Report project as malware

Release files for osteoid 0.7.4

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for osteoid 0.7.4
File Size Uploaded
osteoid-0.7.4.tar.gz 418.3 kB Details

Built distributions (wheels)

Table of built distributions (wheels) for osteoid 0.7.4
File
osteoid-0.7.4-cp315-cp315-win_amd64.whl 338.6 kB CPython 3.15 CPython 3.15 Windows x86-64 Details
osteoid-0.7.4-cp315-cp315-musllinux_1_2_x86_64.whl 1.2 MB CPython 3.15 CPython 3.15 Linux musl 1.2+ x86-64 Details
osteoid-0.7.4-cp315-cp315-musllinux_1_2_aarch64.whl 1.1 MB CPython 3.15 CPython 3.15 Linux musl 1.2+ ARM64 Details
osteoid-0.7.4-cp315-cp315-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl 165.6 kB CPython 3.15 CPython 3.15 Linux glibc 2.24+ x86-64, Linux glibc 2.28+ x86-64 Details
osteoid-0.7.4-cp315-cp315-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl 155.1 kB CPython 3.15 CPython 3.15 Linux glibc 2.24+ ARM64, Linux glibc 2.28+ ARM64 Details
osteoid-0.7.4-cp315-cp315-macosx_11_0_arm64.whl 139.8 kB CPython 3.15 CPython 3.15 macOS 11.0+ ARM64 Details
osteoid-0.7.4-cp315-cp315-macosx_10_15_x86_64.whl 149.9 kB CPython 3.15 CPython 3.15 macOS 10.15+ x86-64 Details
osteoid-0.7.4-cp314-cp314t-win_amd64.whl 343.2 kB CPython 3.14 CPython 3.14 free-threading Windows x86-64 Details
osteoid-0.7.4-cp314-cp314t-musllinux_1_2_x86_64.whl 1.2 MB CPython 3.14 CPython 3.14 free-threading Linux musl 1.2+ x86-64 Details
osteoid-0.7.4-cp314-cp314t-musllinux_1_2_aarch64.whl 1.1 MB CPython 3.14 CPython 3.14 free-threading Linux musl 1.2+ ARM64 Details
osteoid-0.7.4-cp314-cp314t-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl 166.9 kB CPython 3.14 CPython 3.14 free-threading Linux glibc 2.24+ x86-64, Linux glibc 2.28+ x86-64 Details
osteoid-0.7.4-cp314-cp314t-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl 158.9 kB CPython 3.14 CPython 3.14 free-threading Linux glibc 2.24+ ARM64, Linux glibc 2.28+ ARM64 Details
osteoid-0.7.4-cp314-cp314t-macosx_11_0_arm64.whl 144.5 kB CPython 3.14 CPython 3.14 free-threading macOS 11.0+ ARM64 Details
osteoid-0.7.4-cp314-cp314t-macosx_10_15_x86_64.whl 154.5 kB CPython 3.14 CPython 3.14 free-threading macOS 10.15+ x86-64 Details
osteoid-0.7.4-cp314-cp314-win_amd64.whl 338.6 kB CPython 3.14 CPython 3.14 Windows x86-64 Details
osteoid-0.7.4-cp314-cp314-musllinux_1_2_x86_64.whl 1.2 MB CPython 3.14 CPython 3.14 Linux musl 1.2+ x86-64 Details
osteoid-0.7.4-cp314-cp314-musllinux_1_2_aarch64.whl 1.1 MB CPython 3.14 CPython 3.14 Linux musl 1.2+ ARM64 Details
osteoid-0.7.4-cp314-cp314-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl 163.9 kB CPython 3.14 CPython 3.14 Linux glibc 2.28+ x86-64, Linux glibc 2.24+ x86-64 Details
osteoid-0.7.4-cp314-cp314-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl 154.9 kB CPython 3.14 CPython 3.14 Linux glibc 2.24+ ARM64, Linux glibc 2.28+ ARM64 Details
osteoid-0.7.4-cp314-cp314-macosx_11_0_arm64.whl 139.7 kB CPython 3.14 CPython 3.14 macOS 11.0+ ARM64 Details
osteoid-0.7.4-cp314-cp314-macosx_10_15_x86_64.whl 149.9 kB CPython 3.14 CPython 3.14 macOS 10.15+ x86-64 Details
osteoid-0.7.4-cp313-cp313-win_amd64.whl 328.6 kB CPython 3.13 CPython 3.13 Windows x86-64 Details
osteoid-0.7.4-cp313-cp313-musllinux_1_2_x86_64.whl 1.2 MB CPython 3.13 CPython 3.13 Linux musl 1.2+ x86-64 Details
osteoid-0.7.4-cp313-cp313-musllinux_1_2_aarch64.whl 1.1 MB CPython 3.13 CPython 3.13 Linux musl 1.2+ ARM64 Details
osteoid-0.7.4-cp313-cp313-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl 163.8 kB CPython 3.13 CPython 3.13 Linux glibc 2.24+ x86-64, Linux glibc 2.28+ x86-64 Details
osteoid-0.7.4-cp313-cp313-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl 154.4 kB CPython 3.13 CPython 3.13 Linux glibc 2.24+ ARM64, Linux glibc 2.28+ ARM64 Details
osteoid-0.7.4-cp313-cp313-macosx_11_0_arm64.whl 139.5 kB CPython 3.13 CPython 3.13 macOS 11.0+ ARM64 Details
osteoid-0.7.4-cp313-cp313-macosx_10_13_x86_64.whl 149.8 kB CPython 3.13 CPython 3.13 macOS 10.13+ x86-64 Details
osteoid-0.7.4-cp312-cp312-win_amd64.whl 328.5 kB CPython 3.12 CPython 3.12 Windows x86-64 Details
osteoid-0.7.4-cp312-cp312-musllinux_1_2_x86_64.whl 1.2 MB CPython 3.12 CPython 3.12 Linux musl 1.2+ x86-64 Details
osteoid-0.7.4-cp312-cp312-musllinux_1_2_aarch64.whl 1.1 MB CPython 3.12 CPython 3.12 Linux musl 1.2+ ARM64 Details
osteoid-0.7.4-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl 163.6 kB CPython 3.12 CPython 3.12 Linux glibc 2.24+ x86-64, Linux glibc 2.28+ x86-64 Details
osteoid-0.7.4-cp312-cp312-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl 155.6 kB CPython 3.12 CPython 3.12 Linux glibc 2.28+ ARM64, Linux glibc 2.24+ ARM64 Details
osteoid-0.7.4-cp312-cp312-macosx_11_0_arm64.whl 139.4 kB CPython 3.12 CPython 3.12 macOS 11.0+ ARM64 Details
osteoid-0.7.4-cp312-cp312-macosx_10_13_x86_64.whl 149.7 kB CPython 3.12 CPython 3.12 macOS 10.13+ x86-64 Details
osteoid-0.7.4-cp311-cp311-win_amd64.whl 326.2 kB CPython 3.11 CPython 3.11 Windows x86-64 Details
osteoid-0.7.4-cp311-cp311-musllinux_1_2_x86_64.whl 1.2 MB CPython 3.11 CPython 3.11 Linux musl 1.2+ x86-64 Details
osteoid-0.7.4-cp311-cp311-musllinux_1_2_aarch64.whl 1.1 MB CPython 3.11 CPython 3.11 Linux musl 1.2+ ARM64 Details
osteoid-0.7.4-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl 163.3 kB CPython 3.11 CPython 3.11 Linux glibc 2.24+ x86-64, Linux glibc 2.28+ x86-64 Details
osteoid-0.7.4-cp311-cp311-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl 154.7 kB CPython 3.11 CPython 3.11 Linux glibc 2.28+ ARM64, Linux glibc 2.24+ ARM64 Details
osteoid-0.7.4-cp311-cp311-macosx_11_0_arm64.whl 137.0 kB CPython 3.11 CPython 3.11 macOS 11.0+ ARM64 Details
osteoid-0.7.4-cp311-cp311-macosx_10_9_x86_64.whl 147.5 kB CPython 3.11 CPython 3.11 macOS 10.9+ x86-64 Details
osteoid-0.7.4-cp310-cp310-win_amd64.whl 325.5 kB CPython 3.10 CPython 3.10 Windows x86-64 Details
osteoid-0.7.4-cp310-cp310-musllinux_1_2_x86_64.whl 1.2 MB CPython 3.10 CPython 3.10 Linux musl 1.2+ x86-64 Details
osteoid-0.7.4-cp310-cp310-musllinux_1_2_aarch64.whl 1.1 MB CPython 3.10 CPython 3.10 Linux musl 1.2+ ARM64 Details
osteoid-0.7.4-cp310-cp310-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl 162.4 kB CPython 3.10 CPython 3.10 Linux glibc 2.24+ x86-64, Linux glibc 2.28+ x86-64 Details
osteoid-0.7.4-cp310-cp310-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl 156.2 kB CPython 3.10 CPython 3.10 Linux glibc 2.24+ ARM64, Linux glibc 2.28+ ARM64 Details
osteoid-0.7.4-cp310-cp310-macosx_11_0_arm64.whl 136.0 kB CPython 3.10 CPython 3.10 macOS 11.0+ ARM64 Details
osteoid-0.7.4-cp310-cp310-macosx_10_9_x86_64.whl 146.2 kB CPython 3.10 CPython 3.10 macOS 10.9+ x86-64 Details
osteoid-0.7.4-cp39-cp39-win_amd64.whl 326.0 kB CPython 3.9 CPython 3.9 Windows x86-64 Details
osteoid-0.7.4-cp39-cp39-musllinux_1_2_x86_64.whl 1.2 MB CPython 3.9 CPython 3.9 Linux musl 1.2+ x86-64 Details
osteoid-0.7.4-cp39-cp39-musllinux_1_2_aarch64.whl 1.1 MB CPython 3.9 CPython 3.9 Linux musl 1.2+ ARM64 Details
osteoid-0.7.4-cp39-cp39-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl 162.2 kB CPython 3.9 CPython 3.9 Linux glibc 2.28+ x86-64, Linux glibc 2.24+ x86-64 Details
osteoid-0.7.4-cp39-cp39-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl 154.3 kB CPython 3.9 CPython 3.9 Linux glibc 2.24+ ARM64, Linux glibc 2.28+ ARM64 Details
osteoid-0.7.4-cp39-cp39-macosx_11_0_arm64.whl 136.1 kB CPython 3.9 CPython 3.9 macOS 11.0+ ARM64 Details
osteoid-0.7.4-cp39-cp39-macosx_10_9_x86_64.whl 146.3 kB CPython 3.9 CPython 3.9 macOS 10.9+ x86-64 Details

Total release size: 26.6 MB

Release files / osteoid-0.7.4.tar.gz

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0.7.4 This release

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