Volumetric Data Python Packages

cloud-volume

Read and write Neuroglancer datasets programmatically.

kimimaro

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

zmesh

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

tinybrain

Image pyramid generation for grayscale and segmentation image resize.

al-dvc

Augmented Lagrangian Digital Volume Correlation (AL-DVC) in Python

igneous-pipeline

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

brook-cu12

TEASAR skeletonization of 3D label volumes on NVIDIA GPUs

chunkflow

Compose chunk operators to create a pipeline for local or distributed petabyte-scale computation

surforama

a tool for using surfaces to explore volumetric data in napari

pytorch3dunet

3D U-Net model for volumetric semantic segmentation written in pytorch

contact-points

Find contact points in a 3D Volume.

quanfima

Quanfima (Quantitative Analysis of Fibrous Materials)

pytorch3dunet-spotmax

3D U-Net model for volumetric semantic segmentation written in pytorch

pytorch3dunet-smax

3D U-Net model for volumetric semantic segmentation written in pytorch