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webKnossos Python API

Python API for working with webKnossos datasets, annotations, and for webKnossos server interaction.

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
  • executing any of the wkcuber operations from below from your code

webKnossos cuber (wkcuber) 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