AI-based automated segmentations

Full training loop with creating annotations in WEBKNOSSOS, training a model as a background process and performing inference of a dataset.One-button solutions with pre-trained models for several segmentation tasks in EM including neurons, synapses, nuclei, mitochondria.

More segment statistics

Adding more available segment statistics such as surface areas, centroids, sphericities.

Collaborative proof-reading

Task system for proof-reading.Materialization of proof-read segments.

Advanced 3D annotation tools

Region growing annotation tool in 3D.Visualisation and annotation along tilted planes

Multi-modal images and analysis

Visualizing layers of different modalities (e.g. light microscopy, µCT, EM) in a single view.Map all modalities in a single coordinate space with affine and non-linear transformations.Create transformations with rotate, scale, and translate tools.

Single-tile stack alignment

Automatically align datasets upon upload to WEBKNOSSOS.
Please contact us for multi-tile alignments.

Time series

Support for importing time series data into webKnossos (5D = 3D + channels + time).
Support for selecting time points via a slider in the UI.

Segment statistics

Calculating and showing statistics about imported and created segmentations.
Statistics will include information per segment such as volume, surface area, centroids, bounding boxes.

Zarr v3 support

Accessing dataset in the Zarr v3 format including sharding.

AI-based quick select

Draw a rectangle around an object and fill it automatically with MetaAI's Segment Anything model.

Segmentation proof-reading

Fix split and merge errors by editing the underlying supervoxel graph of a segmentation.
Works best with segmentations from Voxelytics.

Single sign-on integration

OpenID Connect (OIDC) authentication support.

Quick select

Draw a rectangle around an object and fill it automatically with a floodfill algorithm.

Dataset management

Organize datasets into folders, attach permissions to folders.
Add metadata to datasets, folders and search by metadata.

Zarr streaming

Stream datasets and annotations from webKnossos to other tools via the Zarr file format

Import Zarr and N5

Import Zarr and N5 datasets. Use the OME-NGFF format to define downsampling pyramids and metadata.

64-Bit segmentations

Support for 64-Bit segmentations.

Segment colors

Select custom colors for segments.

Shared annotations

Better collaboration by enabling write access to a shared annotation within a team of annotators.

Volume interpolation

Create a volume annotation on a section, skip a few sections, draw again and interpolate in between.

Connectome Viewer

Visualize agglomerate skeletons and synapses. List synaptic connections of neuron and jump from one neuron to the next.

Python library

Create, upload and access datasets and annotations from Python.