WEBKNOSSOS for Imaging Facilities
Upload and manage large 3D datasets effortlessly
Drag and drop your data for quick uploads, organize datasets with folder structures, tags, and metadata, and set access permissions.
Visualize your data online - anytime, anywhere
Access your data from any device with an internet connection, including laptops and tablets, and experience fast, seamless browsing.
Annotate and process your data
Use skeleton and volume annotation tools for efficient image data processing. Automate your analysis with the AI tools of WEBKNOSSOS.
Collaborate and share with ease
Collaborate seamlessly with your team throughout the entire process. Send private links to clients at any stage for feedback or updates.
How it works
1. Upload your data to the cloud
Easily upload large 3D image datasets using drag-and-drop, supporting TIFF stacks and other formats of your choice.
2. Align your data directly in WEBKNOSSOS
Align your volume EM data effortlessly with our intuitive alignment tool. For complex alignments, use our hassle-free alignment services for expert precision.
3. Annotate and process your data
Leverage WEBKNOSSOS's annotation tools to accelerate your analysis. Use smart features like the AI quick-select tool, or automate segmentation with pretrained models—or even train custom models tailored to your data.
4. Collaborate seamlessly with your team
Tackle large analysis projects together, sharing annotations and data insights. Team members can communicate and access shared links from their own devices, ensuring everyone is on the same page.
5. Share data and receive client feedback
Keep clients involved by sending private links at any stage of the project. Each link is secure, allowing clients to view the exact data location and annotations you're discussing.
6. Deliver and hand over seamlessly
Once your project is complete, clients can continue exploring their data on WEBKNOSSOS or download it in preferred formats. Since they’ve had ongoing access, handover is simple and requires no extra steps.
Pricing for imaging facilities
Scientific core facilities benefit from customized plans that cater specifically to their needs. Each plan includes "client accounts," allowing you to share project data with clients seamlessly, without additional charges for them. Our flexible pricing options are designed to accommodate both smaller and larger core facilities. For large imaging facilities, WEBKNOSSOS can be installed on-premise, allowing you to use your own storage space.
Small core facilities
from 5,000 €/year
This plan includes 5 users and 1 TB of storage, which are both upgradable and features annotation, collaboration, and data management capabilities.
Adds-on
● additional user account: 500€ per user/year● additional client account: upon request● additional storage: 500€ per TB/year
Large core facilities
from 10,000 €/year
This plan includes 10 users and 5 TB of storage, also upgradable. This plan features advanced proofreading capabilities and flexible deployment options.
Adds-on
● additional user account: 500€ per user/year● additional client account: upon request● additional storage: 500€ per TB/year
Key features
Visualize massive datasets–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
Securely share data with 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.
Analyze your data directly online
Take measurements within your data. Mark interesting locations or bounding boxes. Create segmentations with manual brush or trace tools. Visualize segmented objects as mesh through the integrated mesh generation.
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.
Use the segment statistics and keep track of the number of annotated segments, their sizes, volumes, locations, and more.
Example: Annotations and EM data from Schmidt et al. 2017
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 wklink.org short-links from Motta et al. 2019 (Science)
Automate your work with our Python library
Use our free WEBKNOSSOS Python library to up/download datasets and annotations, work with WEBKNOSSOS datasets locally, and convert image stacks. The Python library seamlessly integrates WEBKNOSSOS in your existing data science workflows for training data generation, machine learning model training and volumetric data visualization.
Read the documentation.
Example: Skeleton approximation of an automatically segmented neuronEM data from Motta et al. 2019, segmentation by scalable minds
Interoperate with your favorite tools
WEBKNOSSOS supports a growing list of data formats for import. 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.
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
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