Skeletonisation

webKnossos is an open-source data sharing and annotation platform for tera-scale 2D and 3D image datasets.

The core features of webKnossos are:

• fast 3D data streaming
• share links to specific locations in the data
• uniquely fast skeleton annotation (flight mode) and
• efficient volume annotation
• mesh rendering
• collaboration and sharing tools

webKnossos facilitates image analysis workflows on multi-terabyte datasets, including visualization of raw and multi-modal microscopy data, distributed training data generation and proof-reading of automatic segmentation.

As a scientific resource, webknossos.org serves as a database for published image datasets including their annotations.

Blood vessels tracing in 3D image from 3D Gaussian blurring (user defined radius), local thresholding (user defined radius and offset) and 3D skeletonization. Dockerized version for BIAFLOWS,

Blood vessels tracing in 3D image from Tubeness filtering (user defined scale), 3D opening (radius set to 2), thresholding (user defined level) and 3D skeletonization.