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Python API and CLI tools for working with WEBKNOSSOS datasets, annotations and server interactions. Includes converter to OME-Zarr.

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WEBKNOSSOS-libs

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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.

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