Visualize your data–from anywhere

Upload your 2D or 3D datasets to webKnossos and access them from wherever you have an internet connection. Enjoy the fast browsing speeds of webKnossos.

webKnossos works with all sorts of electron microscopy images, X-ray tomographies (CT), fluorescence microscopy images, and MRI.

Example: EM data from Motta et al. 2019, segmentation by scalable minds

Create and visualize segmentations

Create volume annotations (i.e. segmentations) with manual brush or trace tools. Download the annotations to train a machine learning model or for visualization purposes.  

Visualize segmented objects as mesh through the integrated mesh generation. Explore dense segmentations with colored and patterned maps. 

Get annotation help from your collaborators. Use the task/project system to distribute tasks to multiple annotators. If you don't have annotators, you can hire our annotation services directly through webKnossos.

Example: EM data from Motta et al. 2019, segmentation by scalable minds

Skeletonize, measure, and quantify neurons 

Create skeleton annotations of neurons, measure their path lengths and organize these skeletons in hierarchical groups. 

Try out the unique flight mode for high-speed tracing of axons or dendrites. Trained annotator crowds achieve tracing speeds of 1.5 ± 0.6 mm/h for axons and 2.1 ± 0.9 mm/h for dendrites in 3D electron microscopy data. Read more in the webKnossos paper.

Collaborate on annotations with your colleagues. Use the task/project system to distribute tasks to multiple annotators. If you don't have annotators, you can hire our annotation services directly through webKnossos.

Example: Annotations and EM data from Schmidt et al. 2017

Share your data with collaborators

Invite your colleagues and collaborators to webKnossos to share your data with them. Because your data is in the cloud, every dataset and annotation has a link that you can share. 

No worries, by default your data is only privately accessible by you and collaborators you choose. Use token-protected links to share data with reviewers or outside collaborators.

Interoperate with your favorite tools

Download your data and annotations from webKnossos to work with them in other tools. webKnossos supports standard formats (e.g. TIFF, STL, N5/ZARR, CSV) for exports.

Work with the webKnossos file formats in Python or MATLAB, with our open-source libraries. Learn more in the user documentation.

Publish your data alongside your publication

Tell your story with data. Link directly from a figure in your publication to that location in webKnossos. Readers will be able to explore your annotations and understand the context of your findings. 

WEBKNOSSOS is an excellent platform for publishing large datasets because readers can freely browse through your data and build upon it. 

Example: Figures with wklink.org short-links from Karimi et al. 2020

Never lose your work

WEBKNOSSOS auto-saves annotations every 30s and keeps a versioned history of all annotations. Correcting a mistake is just one click away.

Annotation data on webKnossos is externally backed up daily. For paid plans, there is an option to back up datasets as well.

You can always download your annotations or datasets in accessible formats.

Example: EM data and annotations from Helmstaedter et al. 2013

Support for many modalities

WEBKNOSSOS works with all sorts of 2D and 3D image modalities including multi-channel data.

Examples (from left): Fluorescence microscopy from Drawitsch et al. 2018, Synchrotron X-Ray Tomography from Kuan et al. 2020 and MRI from Lüsebrink et al. 2017