Frequently Asked Questions

Look through the answers to the most popular questions.Please contact us if you have any other question.

How do I get started?

You can try webKnossos for free here on Create a free account today.
All webKnossos features can be used with free accounts. Upload your own data or work with available published datasets. We are also happy to integrate your dataset in the publication gallery. 
You can learn more about webKnosssos in the user documentation. Alternatively, get in touch with us and one of our webKnossos experts will help you get started.

What about open-source?

webKnossos is an open-source project. Check out the instructions on Github to deploy your own instance of webKnossos.
If that is too much trouble, you can find all features here on as well.

I need more than 10GB of storage for my datasets.

Our Basic plan includes 10 GB of storage for private datasets in order for you to get started.
We have a Pilot program that offers more storage. You can apply for the program at any time.
The Premium plan includes 1TB of storage and is upgradeable through paid add-ons.
Additionally, you may install a local data adapter to stream data from your own infrastructure to webKnossos for free.

What is the difference between Knossos and webKnossos?

While webKnossos and Knossos share some of the roots, they are two distinct software tools for viewing and annotating 3D datasets developed by different teams.
webKnossos supports a wide array of popular data formats and is used for creating both skeleton and volume annotations. As browser-based application, it is easy to collaborate with others, share links to datasets and publish datasets for other to review.

Can I further analyze my annotations outside of webKnossos with Python/MATLAB?

Yes, you can. webKnossos allows the download and export of skeleton annotations as NML files and segmentations/volume data as binary/wkw files.
See the documentation on tooling for a recommendation of Python/MATLAB libaries to work with the webKnossos standard formats.
We offer a Custom hosting plan, where datasets can be directly stored in your data center. Get in touch with us to learn more.

Why should I trust scalable minds with my data?

Data security is one of our top priorities. All private datasets uploaded on are stored securely and NOT shared with anyone. webKnossos has fine-grained permissions for individual users, teams, and datasets to control the access. Only authorized users within your organization will be able to access your datasets and annotations. Read our privacy statement.
We offer Custom hosting services, where datasets can be directly stored in your data center. Get in touch to learn more.

Where is my data stored?

All datasets uploaded on are stored securely in the scalable minds cloud infrastructure in Germany. Hosted 100% on renewable energy.
We offer Custom hosting services, where datasets can be directly stored in your data center. Get in touch with us to learn more.

Which payment methods are available?

You can get started with a free account without any payment methods.
For paid accounts, we accept payment through credit card, PayPal and SEPA bank transfer. Billing is on an annual basis.

Can I change my plan at a later time? Can I cancel anytime?

Paid plans are billed annually. You can cancel your plan before the end of your billing cycle. 
You may upgrade your plan at any point in time. We are happy to assist you with migrating your data if necessary.

I am looking for a custom webKnossos setup.

webKnossos can be set up to accommodate flexible deployment scenarios. Over the years we have worked with different research institutes and have tackled a diverse set of challenges. Custom data formats, petabyte-scale datasets, on-premise or cloud storage, file system tuning, monitoring...
Our Custom hosting services are right for you. Talk to our webKnossos experts about custom solutions.

Where can I learn more about webKnossos?

webKnossos offers a wide array of tools to manage large 3D datasets and annotate them efficiently. Learn more about webKnossos and its functionality on our features overview page.
Check out the webKnossos user documentation to learn more about all annotation modes and their settings. Alternatively, get in touch with us and one of our webKnossos experts will help you get started.
Make sure to follow webKnossos on Twitter to get updates about the latest features.

I need a new functionality not yet available in webKnossos

We constantly develop new features and continuously improve webKnossos. As an open-source project, you can extend webKnossos yourself. webKnossos also comes with a rich frontend API and REST interface for scripting new workflows. Alternatively, you can hire us to help you with custom feature development.
We are always interested in learning about new ideas and gathering feedback. Get in touch with us and let us know.

Who develops and runs webKnossos?

webKnossos is an open-source project developed by scalable minds in collaboration with the Max-Planck-Institute for Brain Research.
All hosting plans on this website are executed and handled exclusively by scalable minds.

How can I access published datasets on

There is a collection of published datasets on All users may freely browse the image datasets and accompanying annotations without a login. Creating a free account will allow to download the data and create custom annotations on top of these datasets.

Looking for Automated Image Analysis?

Check out our image analysis services. Reconstruct rich information from microscopy images with machine learning-based tools. Automate tasks such as image alignment, registration, dense segmentation, and object detection.