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