Help your team to collaborate and publish

Make sure everybody has access to the data, by keeping it in one place. Invite and manage outside collaborators.Publish your data alongside your paper.


WEBKNOSSOS for Research Group Leaders


Foster collaboration within your team

Since the data is available through a website, all team members can access it from wherever they are. Collaboratively annotate the data and send links to specific locations within the dataset.

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

Example: EM and annotations from Schmidt et al. 2017

Visualize your data–from anywhere

Access massive datasets from wherever you are. Enjoy the fast browsing speeds of WEBKNOSSOS.

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

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


Get your datasets annotated

Use the skeleton tools to trace neurons or mark locations in the dataset. Try out the unique flight mode for high-speed tracing of axons or dendrites. Measure path lengths and organize skeletons in hierarchical groups.

Use the volume annotation features to generate training data for a segmentation model or pixel classifier.

Use the task/project system to manage annotation projects with multiple annotators. If you don't have annotators, you can hire our annotation services directly through WEBKNOSSOS.

Example: Ground truth volume annotations from Berning et al. 2015

Provide secure access to outside collaborators

Invite collaborators or annotators into your organization. Manage users in teams and set role-based dataset permissions.

Send token-protected links to outside collaborators or reviewers.

The data stays safe in WEBKNOSSOS: By default users are not allowed to download the data unless you enable it.


Publish datasets to the community–when ready

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 including segmentations and training data. Viewers can freely browse through your data and build upon it. 

Example: Figures with short-links from Motta et al. 2019 (Science)

Follow the progress of your team

Receive links to annotations or interesting locations in the data. Review predictions or segmentations from your machine learning projects.

Include permanent links in your lab notebooks for documentation and reproducibility.

Example: EM data from Motta et al. 2019, segmentation (left) and affinity predictions (right) by scalable minds


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

Manage your massive datasets in one place

Use WEBKNOSSOS as a centralized storage for your large-scale datasets. Stop scattering data around endless hard-drives or storage servers. WEBKNOSSOS easily scales to petabytes of data.

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.

Or, work directly with the WEBKNOSSOS' efficient file formats in Python or MATLAB, with our open-source libraries. Learn more in the user documentation.


Support for many modalities

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

    Scanning electron microscopy (SEM)
    Transmission electron microscopy (TEM)
    Serial block-face scanning electron microscopy (SBEM)
    Focused ion beam scanning electron microscopy (FIB-SEM)
    Serial section electron microscopy (ssSEM, S3EM, ssTEM)
    X-ray tomography (CT) and Micro-CT (µCT)
    Magnetic resonance imaging (MRI)
    Fluorescence microscopy

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

Get started and upload your first dataset for free

A story about collaboration, continents, and the struggles of big data

Embark on a journey with two scientists in London as they navigate the challenges of managing vast datasets from a serial electron microscope. Witness their discovery of WEBKNOSSOS, the tool that will streamline their data analysis and collaboration, even as their research takes them across continents. Watch on YouTube

Follow us on Twitter and Mastodon to get updates on the latest features