WEBKNOSSOS-libs

WEBKNOSSOS Python API

API

Python API for working with WEBKNOSSOS datasets, annotations, and for WEBKNOSSOS server interactions.

Use this for:

• reading/writing/manipulating raw 2D/3D image data and volume annotations/segmentation in WEBKNOSSOS wrap (*.wkw) format
• handling/manipulation of WEBKNOSSOS datasets
• reading/writing/manipulating WEBKNOSSOS skeleton annotations (*.nml)
• up- & downloading annotations and datasets from your WEBKNOSSOS instance

Read more in the docs.

CLI

CLI tool for creating and manipulating WEBKNOSSOS WKW datasets. WKW is a container format for efficiently storing large-scale 3D images as found in microscopy data.

Use this for:

• converting Tiff-stacks and other data formats for volume image data to WEBKNOSSOS-compatible *.wkw files from the CLI
• up/downsampling of *.wkw files to different magnification levels (image pyramid) from the CLI
• compressing your *.wkw files to save disk space from the CLI

Read more in the docs.

Cluster Tools

The cluster_tools package provides python Executor classes for distributing tasks on a slurm cluster or via multi processing.