VISUALIZE · ANNOTATE · SHARE · ANALYZE WITH AI

VISUALIZE · SHARE · ANNOTATE · ANALYzE

Large-scale 3D microscopy, right in your browser

WEBKNOSSOS lets labs explore, annotate, and reconstruct volume electron and light microscopy datasets, from a single volume to petabyte-scale connectomics. Share a dataset with a link, and divide the work across your team.

Create a free account

Explore a public dataset

Data: Motta et al., Science 2019.

VISUALIZE

See your data at full resolution, in the browser.

Open a dataset and move through it at native resolution, from gigabytes to petabytes, with nothing to install. Built for volume EM, and at home with light microscopy, X-ray, and correlative microscopy.

Learn more about data sources, working with meshes, and correlating datasets.

Data: Berg et al., bioRxiv 2025.

VISUALIZE

See your data at full resolution, in the browser.

Learn more about data sources, working with meshes, and correlating datasets.

Data: Motta et al., Science 2019.

ANNOTATE

Trace and segment in one workspace.

Skeleton tracing and volume segmentation side by side, with AI quick-select and interpolation speeding up the slow parts. Every change autosaves, with full version history.

Learn more about skeleton & volume annotations, and segment measurements.

Data: Motta et al., Science 2019.

ANNOTATE

Trace and segment in one workspace.

Skeleton tracing and volume segmentation side by side, with AI quick-select and interpolation speeding up the slow parts. Every change autosaves, with full version history.

Learn more about skeleton & volume annotations, and segment measurements.

Data: Motta et al., Science 2019.

COLLABORATE

Share the data, split the work.

Send a link that opens the exact view you’re looking at. No downloads, no file versions. Work on the same datasets as your colleagues, and divide large annotation jobs across the team.

Learn more about users and permissions, and collaboration in WEBKNOSSOS.

Data: Motta et al., Science 2019.

COLLABORATE

Share the data, split the work.

Send a link that opens the exact view you’re looking at. No downloads, no file versions. Work on the same datasets as your colleagues, and divide large annotation jobs across the team.

Learn more about users and permissions, and collaboration in WEBKNOSSOS.

Data: Motta et al., Science 2019.

ANALYZE WITH AI

Segment automatically, proofread together

Run pre-trained models to segment neurons and mitochondria, or train your own. Then proofread the result together, turning a rough segmentation into a connectome you can publish.

Learn more about automated image processing and proofreading.

Data: Motta et al., Science 2019.

ANALYZE WITH AI

Segment automatically, proofread together

Run pre-trained models to segment neurons and mitochondria, or train your own. Then proofread the result together, turning a rough segmentation into a connectome you can publish.

Learn more about automated image processing and proofreading.

Data: Motta et al., Science 2019.

WORKFLOW

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.

WORKFLOW

Supporting your work from raw images to analysis insights

Acquire

Import from SEM, multi-SEM, and light microscopy, then combine modalities in one place.

Align

Align and register serial sections directly in WEBKNOSSOS, before you segment. No separate tool.

Annotate

Paint volumes with AI quick-select and trace skeletons in the same workspace. Work on one annotation together, each from your own computer.

Analyze

Segment neurons and mitochondria with pre-trained models, or train your own on your annotations. No pipeline to build.

Proofread

Fix split and merge errors on large segmentations by editing the supervoxel graph, collaboratively and in near real time.

Publish

Share a dataset with a link, with access control so it stays private until you choose. Export publication-ready animations and figures.

Interoperability

Stream your data out as OME-Zarr so tools like napari, Fiji, and Neuroglancer can read it. Script and automate everything through the Python library and REST API.

Zarr

Load OME-Zarr (NGFF) datasets, and export your data back out as a Zarr stream. WEBKNOSSOS also reads WKW, N5, and Neuroglancer Precomputed.

Cloud storage

Stream datasets directly from Amazon S3, Google Cloud Storage, or an HTTP server. Your data stays where it is and loads read-only, without counting against your storage quota.

CASE STUDIES

Published research runs on WEBKNOSSOS

Labs use WEBKNOSSOS to get from raw data to results that reach the literature. Here are two: a large-scale connectomic comparison, and a correlative microscopy study across seven modalities.

CASE STUDIES

Published research runs on WEBKNOSSOS

Labs use WEBKNOSSOS to get from raw data to results that reach the literature. Here are two: a large-scale connectomic comparison, and a correlative microscopy study across seven modalities.

CONNECTOMICS

Routine connectomic reconstructions

Loomba et al. reconstructed nine datasets fully automatically in a few days, revealing differences in the interneuron network between mouse and human.

Learn more

CONNECTOMICS

Routine connectomic reconstructions

Loomba et al. reconstructed nine datasets fully automatically in a few days, revealing differences in the interneuron network between mouse and human.

Learn more

CORRELATIVE MICROSCOPY

Sample prep and warping accuracy in the olfactory bulb

After imaging one brain with seven modalities, Zhang et al. explored how to generate reliable correlative maps, and the central role WEBKNOSSOS played in their workflow.

Learn more

CORRELATIVE MICROSCOPY

Sample prep and warping accuracy in the olfactory bulb

After imaging one brain with seven modalities, Zhang et al. explored how to generate reliable correlative maps, and the central role WEBKNOSSOS played in their workflow.

Learn more

GLOBAL CONNECTOMICS COMMUNITY

Trusted by labs worldwide

From university cores to national facilities, WEBKNOSSOS keeps massive microscopy datasets accessible where collaboration happens.

GLOBAL CONNECTOMICS COMMUNITY

Trusted by labs worldwide

From university cores to national facilities, WEBKNOSSOS keeps massive microscopy datasets accessible where collaboration happens.

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

David Berson

Professor at Brown University

“WEBKNOSSOS enables extraordinary ease in team annotations of our connectomic datasets.” –

Gregg Wildenberg

Staff Scientist, University of Chicago

“WEBKNOSSOS is very useful for safely storing large datasets and managing access across multiple users.” –

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 the article.

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 the article.

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.”

Luke Noon

Team leader of the Metabolic Growth Signals and Regenerative Medicine Laboratory

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

David Berson

Professor at Brown University

“WEBKNOSSOS enables extraordinary ease in team annotations of our connectomic datasets.” –

Gregg Wildenberg

Staff Scientist, University of Chicago

“WEBKNOSSOS is very useful for safely storing large datasets and managing access across multiple users.” –

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 the article.

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 the article.

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.”

Luke Noon

Team leader of the Metabolic Growth Signals and Regenerative Medicine Laboratory

RESEARCH & PRODUCT