Knossos and WEBKNOSSOS

Knossos and WEBKNOSSOS share common roots. Both software tools are developed by different teams and now have different feature sets. The core user interface of displaying and browsing microscopy data as well as the NML format for skeleton annotations in WEBKNOSSOS have been inspired by Knossos.

WEBKNOSSOS includes many useful features, including web-based sharing, fast skeletonization, hierarchical tree grouping, mesh visualization, proof-reading features, task management, time tracking, automatic dataset import, and support for many modalities.

WEBKNOSSOS remains compatible with the data formats of Knossos and makes it easy to switch.


Compatibility with Knossos

NML files


Importing existing NML files into WEBKNOSSOS works out of the box. There are small differences in the file formats of the two software tools, but WEBKNOSSOS will automatically make your file compatible.

Knossos datasets


The upload system of WEBKNOSSOS will convert a Knossos dataset into a more efficient file format. This is an automatic process. You can also convert Knossos datasets offline using our Python-based cubing tool.

Many published datasets are already available in our publication gallery.

Features of WEBKNOSSOS


Fast skeleton annotation

Fast and precise skeleton annotation with flight mode. Organize trees in hierarchical groups. Optimized for big annotation with millions of nodes.


Share datasets and annotations

Access your data from anywhere you are. Send links to colleagues. Collaborate on annotations. Manage large annotation projects, including time-tracking.


Volume annotation and meshes

Create segmentations (i.e. volume annotations) with brush and trace tools. Visualize segments with automatic mesh generation.

Text element



Fix over-segmentations with merger mode and correct problems with brush tools.


Many modalities

Support for fluorescence microscopy, electron microscopy, Micro-CT (µCT) and MRI.


Scalable to petabytes

Efficiently work with datasets that are larger than your hard disk.

Get started and upload your first dataset for free