Visualize, share, and annotate your large 3D images online

Upload your data and share links with colleagues. Collaboratively create skeleton and volume annotations, all from your browser. Optimized for multi-terabyte datasets.

Attributions: Zheng et al., Cell 2018, Santella et al., eLife 2022, Drawitsch et al., eLife 2018, Loomba et al., Science 2022, Payne et al., Science 2020

"WEBKNOSSOS is the best web-based tool out there for integrated team-based annotation, proofreading, display, and output of serial EM data." - Read more.

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David Berson

Professor at Brown University

"WEBKNOSSOS enables extraordinary ease in team annotations of our connectomic datasets." - Read more.

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Gregg Wildenberg

Staff Scientist, University of Chicago

"WEBKNOSSOS is very useful for safely storing large datasets and managing access across multiple users." - Read more.

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Carles Bosch

Principal Laboratory Research Scientist, Francis Crick Institute

"With WEBKNOSSOS, I can visualize the ground truth and my predictions (skeletons or volume annotations) as overlapping layers." - Read more.

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Valentin Pinkau

Data scientist at scalable minds

"We use WEBKNOSSOS a lot for data visualization, annotation, and result evaluation. It is our primary tool for volume annotations." - Read more.

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Sahil Loomba

Post-doc research scientist, Max Planck Institute for Brain Research

"WEBKNOSSOS played a central role in our research. We stored all of our datasets there and used it for data sharing, collaboration, and annotation." 

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Luke Noon

Team leader of the Metabolic Growth Signals and Regenerative Medicine Laboratory

Visualize your large 3D images

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Fast browsing

Specialized storage, streaming, and rendering technology enable fast browsing speeds on your work computer and home-office laptop. 
No additional installations beyond the browser are needed, making it effortless to collaborate with others.

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Mesh visualization

Explore your data in 3D with automatically generated meshes. WEBKNOSSOS generates meshes from volume annotations or pre-computed segmentations.

Use the screenshot feature to create figures or export the meshes in your favorite 3D rendering software (e.g., Blender, Amira, Cinema4D).

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Volume Electron microscopy

WEBKNOSSOS features a UI optimized specifically for Volume Electron Microscopy. 
Effortlessly load your large raw EM data and seamlessly navigate through it using the viewports. Observe your segments in 3D after computing meshes. 

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Microscopy modalities

WEBKNOSSOS works great for light-microscopy images including light-sheet microscopy, confocal microscopy, and more. 
Visualize your 2D or 3D data using different channels as layers. Adjust contrast, gamma value, opacity, and blend modes to optimize your resulting image.

Annotate objects

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Volume annotations

Use the AI-based quick-select and the interpolation feature to speed up 3D annotations. Refinewith manual brush and trace tools. Download the annotations to train a machine learning model or for visualization purposes.
Visualize segmented objects as meshes through the integrated mesh generation. Explore dense segmentations with colored and patterned maps.

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Skeleton annotations

Create skeleton annotations of neurons or vasculature, represented as line segments, and measure their path lengths. Organize these skeletons into hierarchical groups. Attach comments to nodes to mark interesting locations in your data.
Experience the unique Flight Mode, designed for high-speed tracing of axons or dendrites. Trained annotator crowds achieve impressive 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. For more details, refer to the WEBKNOSSOS paper.

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Autosave and history

WEBKNOSSOS automatically saves annotations every 30 seconds and maintains a versioned history of every action across all annotations. Correcting a mistake is as simple as clicking "undo."

In addition, annotation data on WEBKNOSSOS is externally backed up on a daily basis. For users with paid plans, there is an option to back up datasets as well.

Collaborate

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Collaborative annotations

Collaborate seamlessly with your colleagues on a single annotation, each working from your own computers. No need to exchange multiple versions or share a single computer. 

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Sharing via link

Easily share your data with colleagues or the world with just two clicks. Thanks to the cloud-based nature of WEBKNOSSOS, every dataset and annotation has a shareable link that allows for easy sharing.

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Dataset management

Leverage WEBKNOSSOS as a centralized storage solution for all your large-scale image datasets. Say goodbye to scattered data across numerous hard drives or storage servers. WEBKNOSSOS effortlessly scales to handle petabytes of data.
Ensure secure management of datasets within your organization with fine-grained user access levels and the ability to create subteams. WEBKNOSSOS helps you maintain data security while streamlining dataset management.

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Interoperability

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. Import your remotely stored datasets as Zarr, N5 or Neuroglancer Precomputed directly in WEBKNOSSOS.
Work with the WEBKNOSSOS file formats in Python using our open-source libraries. For more information on tooling and implementation, refer to the documentation

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Tasks and project management

Efficiently manage annotation tasks by setting up assignments for your annotators and utilizing auto-assignment to distribute the workload. Monitor the progress of the annotations using monitoring reports, allowing you to stay updated on the status of the tasks. For further processing, easily download all the created annotations in a merged file.If you don't have annotators available, you can directly hire our annotation services through WEBKNOSSOS, ensuring access to professional annotation support.

Case studies

Routine connectomic reconstructions with WEBKNOSSOS

Sample Preparation and Warping Accuracy for CMI in the Mouse Olfactory Bulb

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A comparative study by Loomba et al. shows differences in the interneuron network between Mouse and Human. For that, eight datasets were reconstructed fully automatically within a few days.
(Science 2022).

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After imaging a brain using 7 different modalities, Zhang et al. explored how to generate reliable correlative maps. This case study examines the crucial role of WEBKNOSSOS in their research process. (Frontiers, 2022)

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

Supporting your work from raw images to analysis insights 

Make WEBKNOSSOS the central hub for large image data in your lab. Import data from your microscopes. Visualize, manage and collaboratively annotate your data directly in WEBKNOSSOS. Stream your data to other tools for advanced analysis via OME-Zarr support.

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Published datasets on WEBKNOSSOS

Explore remarkable datasets from the scientific community in WEBKNOSSOS.Sign up to build upon the data and create your own annotations.

Your dataset is not in the list?We are happy to host selected public datasets on webknossos.org for free.Please contact us to get the dataset uploaded.

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.

Highlights from our Blog

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New AI-based quick segment tool in WEBKNOSSOS


June 2023

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Reconstructing a kiwi fruit… with SBEM (sort of)


January 2023

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Tutorial on volume annotations with WEBKNOSSOS


May 2023

Need ground truth for your deep learning project?

Check out your manual annotation services. The easiest way to acquire high-quality annotations. 

Looking for Neuron and Connectome reconstruction?

Check out our image analysis services for neuron and connectome reconstructions from volume EM data. Automate tasks such as image alignment, registration, dense segmentation, and object detection.