Volumetric Data Python Packages

cloud-volume

Read and write Neuroglancer datasets programmatically.

zmesh

Marching Cubes & Mesh Simplification on multi-label 3D images.

kimimaro

Skeletonize densely labeled 3D image segmentations with TEASAR. (Medial Axis Transform)

tinybrain

Image pyramid generation for grayscale and segmentation image resize.

igneous-pipeline

Scalable Neuroglancer compatible Downsampling, Meshing, Skeletonizing, Contrast Normalization, Transfers and more.

chunkflow

Composable image chunk operators to create pipeline for distributed computation.

pytorch3dunet

Versatile U-Net implementation for volumetric semantic segmentation written in PyTorch

pytorch3dunet-smax

3D U-Net model for volumetric semantic segmentation use in SpotMAX

pytorch3dunet-spotmax

3D U-Net model for volumetric semantic segmentation use in SpotMAX

contact-points

Find contact points in a 3D Volume.

quanfima

The package for morphological analysis and visualization of fibrous materials.