iiinova — where your digital self keeps evolving

WEBKNOSSOS @webknossos.org · 16/09/2026

💎 Oldy but goldy: viewport navigation in WEBKNOSSOS. Rotate the orthogonal viewports freely for the best angle, jump into Flight mode, and rearrange, maximise or reset your layout any time. #WEBKNOSSOS

010

WEBKNOSSOS @webknossos.org · 10/09/2026

Help your students get familiar with connectomic analysis of retinal neurons! They'll trace retinal ganglion cells and identify bipolar cell inputs - just like professional neuroanatomists. Exercises by Prof. Berson, Brown University. medium.com/webknossos/n... #neuroanatomy #WEBKNOSSOS

medium.com

Neuroanatomy exercises with WEBKNOSSOS

Credits: Prof. David Berson from Brown University

030

WEBKNOSSOS @webknossos.org · 08/09/2026

New feature 🐣 Layer transforms (translation, rotation, and scaling) can now be edited live while viewing or annotating data. Try it out on webknossos.org!

010

WEBKNOSSOS @webknossos.org · 03/09/2026

Got your data in WEBKNOSSOS and a coding agent like Claude? Turn it into a beautiful flythrough video. Let the AI write code to control camera moves, layer opacities and more, and show your audience what you actually see. Learn how in our blog post: home.webknossos.org/blog/creatin...

030

WEBKNOSSOS @webknossos.org · 01/09/2026

Around WEBKNOSSOS in 80 seconds 🌍 Experience fast 3D microscopy data exploration. Annotate with AI, explore 3D meshes, collaborate in real time, manage datasets, and share your research with one click. Sign up for free at webknossos.org!

000

WEBKNOSSOS @webknossos.org · 01/09/2026

💎 Oldy but goldy: dataset management in WEBKNOSSOS. Organise datasets into folders with per-folder permissions, recognize them at a glance with thumbnails, and attach metadata and tags to datasets. #WEBKNOSSOS

000

WEBKNOSSOS @webknossos.org · 25/08/2026

💎 Oldy but goldy: the bounding box tool in WEBKNOSSOS. Create & resize a box, move it with Ctrl, fine-tune the values in the sidebar — then export the data inside, register segments, or auto-generate boxes for AI training. #WEBKNOSSOS

000

WEBKNOSSOS @webknossos.org · 20/08/2026

Maximum Intensity Project is now available in WEBKNOSSOS 🐣 MIP renders your dataset directly in the 3D viewport, by projecting a layer through the volume and keeping the brightest value along each ray. Read the article: home.webknossos.org/blog/mip

002

WEBKNOSSOS @webknossos.org · 18/08/2026

💎 Oldy but goldy: animations in WEBKNOSSOS. Render a video where the EM data shrinks to reveal your 3D meshes — with camera path, resolution and mesh options. Perfect for talks and papers. #WEBKNOSSOS

000

WEBKNOSSOS @webknossos.org · 11/08/2026

💎 Oldy but goldy: 3D meshes in WEBKNOSSOS. Generate them ad-hoc or precompute them, adjust per-segment opacity to reveal organelles, export as STL, and click a mesh to jump straight to that spot in 2D.

000

WEBKNOSSOS @webknossos.org · 04/08/2026

💎 Oldy but goldy: the segments list in WEBKNOSSOS. Organise segments into groups, run batch actions across a whole group, give them custom colors, and read stats — count, volume, surface area, bbox — with CSV export.

000

WEBKNOSSOS @webknossos.org · 09/07/2026

Meet the WEBKNOSSOS Assistant 🤵‍♂️ Ask questions in natural language and get clear answers instantly. Available directly in WEBKNOSSOS through the Help button and throughout our documentation.

000

WEBKNOSSOS @webknossos.org · 07/07/2026

Nuclei and soma detection are now available in WEBKNOSSOS! Try it on webknossos.org.

000

WEBKNOSSOS @webknossos.org · 03/07/2026

“We learned the content in lecture and then actually saw how it applied in real life.” A student in Ahmed Elewa’s cell biology class describes using WEBKNOSSOS to explore real 3D EM data of a C. elegans embryo - turning lecture concepts into hands-on annotation and discovery:

home.webknossos.org

WEBKNOSSOS | Teaching Cell Biology with Real EM Data

May 2026

000

WEBKNOSSOS @webknossos.org · 01/07/2026

The WEBKNOSSOS Python docs are now available via llms.txt. Use your favorite AI assistant to explore the API, learn workflows, and find answers directly from the documentation. docs.webknossos.org/llms.txt

020

WEBKNOSSOS @webknossos.org · 24/06/2026

We’re looking forward to the Connectomics Conference 2026 starting this Sunday and hope to see many of you there! 🧠 Come meet the WEBKNOSSOS team, exchange ideas with fellow researchers, and discuss the future of connectomics research and tooling.

030

WEBKNOSSOS @webknossos.org · 19/06/2026

Working on correlative microscopy workflows? Use skeletons to align landmarks and combine light microscopy and vEM data directly in WEBKNOSSOS. Example dataset (Drawitsch et al., eLife 2018): webknossos.org/links/tNaRtC...

002

WEBKNOSSOS @webknossos.org · 17/06/2026

You can now customize your keyboard shortcuts in WEBKNOSSOS! Go to the user menu → Keyboard Shortcuts to add or edit them. Tip: it also gives you a full overview of all available shortcuts.

000

WEBKNOSSOS @webknossos.org · 08/06/2026

"And most of our users are [...] not necessarily equipped with workstations that can open 60 GB volumes, let alone terabytes. Downloading everything ‘just to see what’s inside’ is unrealistic." Read more about the solution developed at the EMBL P14 beamline: medium.com/webknossos/f...

medium.com

From Beamline to Browser: Automating High-Throughput X-ray Imaging with WEBKNOSSOS at EMBL P14

At the European Molecular Biology Laboratory (EMBL) in Hamburg, the X-ray imaging team working at the P14 beamline on Petra III at DESY has…

020

WEBKNOSSOS @webknossos.org · 04/06/2026

Creating animations in WEBKNOSSOS? You can now include skeletons in your renders. Generate clearer videos for publications, presentations, or sharing your reconstructions. Try it out at webknossos.org now!

001

WEBKNOSSOS @webknossos.org · 02/06/2026

“Students weren’t just annotating - they were thinking critically about what they observed.” In this course, students used WEBKNOSSOS to explore real EM data, segment organelles, analyze cellular asymmetry, and develop biological hypotheses from their own observations. Read more: buff.ly/MckCdVY

011

WEBKNOSSOS @webknossos.org · 28/05/2026

Segment cells in 3D with the Quick Select tool in WEBKNOSSOS! Just click inside a process and WEBKNOSSOS automatically segments it across multiple sections. Adjust the number of Z sections in the toolbar settings (top right).

000

WEBKNOSSOS @webknossos.org · 26/05/2026

“The dataset was already on WEBKNOSSOS, which made it easy to onboard students and start annotating immediately.” @inperience.bsky.social shares how browser-based access to published EM datasets enabled a semester-long collaborative annotation project with ~50 students. Read more: buff.ly/MckCdVY

020

WEBKNOSSOS @webknossos.org · 21/05/2026

Automatically sample bounding boxes for ML training in WEBKNOSSOS. Choose the magnification, number, and size of boxes, and review the generated boxes to adjust any that landed in empty regions. Learn how to choose suitable box sizes and counts for ML training: docs.webknossos.org/webknossos/a...

000

WEBKNOSSOS @webknossos.org · 20/05/2026

"We can produce up to 12 tomograms per hour, and beam time can run for 24 hours straight. So a single user can easily generate multiple terabytes in one session." Read more on how Angelika Svetlove used WEBKNOSSOS to efficiently handle such massive images: medium.com/webknossos/f...

000

WEBKNOSSOS @webknossos.org · 18/05/2026

Did you know you can view and work with time series (N-dimensional) datasets in WEBKNOSSOS? You can even inspect statistics for a specific time point.

000

WEBKNOSSOS @webknossos.org · 15/05/2026

We spoke with @inperience.bsky.social from Miami University about using WEBKNOSSOS in a cell biology course built around real C. elegans vEM data. 48 students annotated cells, generated AI training data, and even contributed to a biological discovery. Read the interview: buff.ly/MckCdVY

012

WEBKNOSSOS @webknossos.org · 13/05/2026

“We can generate data much faster than people can analyze it.” At EMBL P14, synchrotron X-ray tomography produces terabytes per experiment. The bottleneck is no longer acquisition: it’s analysis. Read the full interview with Angelika Svetlove:

medium.com

From Beamline to Browser: Automating High-Throughput X-ray Imaging with WEBKNOSSOS at EMBL P14

At the European Molecular Biology Laboratory (EMBL) in Hamburg, the X-ray imaging team working at the P14 beamline on Petra III at DESY has…

020

WEBKNOSSOS @webknossos.org · 28/04/2026

Managing a connectomics or volume EM project? Validate segmentation on small regions before scaling to the full dataset. Iterate until results are satisfactory.

000

WEBKNOSSOS @webknossos.org · 22/04/2026

Start with a small test bounding box. Validate the segmentation, inspect errors, and only then run the model on the full dataset. A controlled workflow for large-scale EM analysis.

041

WEBKNOSSOS @webknossos.org · 20/04/2026

Applying AI segmentation to a vEM dataset? Through the WEBKNOSSOS AI Grants, selected projects receive compute credits to evaluate segmentation workflows on their data. Reach out with a link to your WEBKNOSSOS dataset and project description at hello@webknossos.org.

010

WEBKNOSSOS @webknossos.org · 16/04/2026

Create figures for your paper with WEBKNOSSOS 🖼️ Customize the view to match your needs: set display modes, adjust the layout, load meshes and edit colors and transparency. These are just a few of the available options for generating publication-ready images. Try it out yourself on webknossos.org!

000

WEBKNOSSOS @webknossos.org · 15/04/2026

“Users can leave Hamburg and continue inspecting their datasets the same day without transferring large volumes of data.” At the P14 beamline, tomography datasets appear in WEBKNOSSOS minutes after reconstruction, allowing users to explore them remotely in the browser. medium.com/webknossos/f...

011

WEBKNOSSOS @webknossos.org · 13/04/2026

All AI analysis workflows in WEBKNOSSOS are now fully documented. Our step-by-step tutorials cover: Alignment Automated segmentation Custom model training Explore the documentation: docs.webknossos.org/webknossos/a...

docs.webknossos.org

AI Automations and Jobs - WEBKNOSSOS Documentation

WEBKNOSSOS integrates several automated workflows that run in the background, ranging from automated segmentation and model training to 3D animations or data handling jobs.

030

WEBKNOSSOS @webknossos.org · 09/04/2026

Running a volume EM core facility? Deliver aligned and segmented datasets with reproducible AI workflows in WEBKNOSSOS - from alignment to custom model training. Support your users with documented, scalable analysis pipelines.

030

WEBKNOSSOS @webknossos.org · 01/04/2026

Segmentation errors often reflect gaps in the training data. Review the ground truth, add missing examples, retrain, and iterate. Custom model training gives you direct control over model behavior. Guidelines for ground truth annotation: buff.ly/w41Ip9e

021

WEBKNOSSOS @webknossos.org · 31/03/2026

🌟Enhancement🌟 Open datasets or jump straight to annotations - right from the command palette. Press Ctrl/Cmd + P from anywhere in the UI, then scroll or start typing to find what you need.

000

WEBKNOSSOS @webknossos.org · 26/03/2026

“And from a facility perspective, everything is automated. No one has to manually convert, upload, organize, or assign permissions.” At EMBL P14, reconstructed tomography datasets are automatically converted and transferred to WEBKNOSSOS through the API. Read more: medium.com/webknossos/f...

031

WEBKNOSSOS @webknossos.org · 25/03/2026

WEBKNOSSOS AI Grant 🔬 We are offering compute credits to support selected research projects applying AI segmentation to volume EM datasets. Interested? Send us a link to your dataset in WEBKNOSSOS and a short description of your analysis goals at hello@webknossos.org.

000

WEBKNOSSOS @webknossos.org · 23/03/2026

Run automated alignment in WEBKNOSSOS and improve the results with manual matches when needed. Maintain control over challenging areas while keeping the workflow efficient. www.youtube.com/watch?v=8IEl...

010

WEBKNOSSOS @webknossos.org · 19/03/2026

Train or refine custom segmentation models directly in WEBKNOSSOS. Annotate ground truth, train the model, test on a small region, iterate, and run on the full dataset.

000

WEBKNOSSOS @webknossos.org · 18/03/2026

Dataset showcase ✨ In this study, Chen et al. (ScienceAdvances, 2025) investigate the ultrastructure and function of lamellar Schwann cells in Pacinian corpuscles, revealing their active role in mechanosensory processing. Explore the segmented dataset in WEBKNOSSOS: wklink.org/3248

010

WEBKNOSSOS @webknossos.org · 12/03/2026

At the EMBL P14 beamline, tomography datasets are automatically transferred into WEBKNOSSOS minutes after reconstruction. Angelika Svetlove explains how the team built this pipeline - and why analysis, not acquisition, is now the main bottleneck. Read the interview:

medium.com

From Beamline to Browser: Automating High-Throughput X-ray Imaging with WEBKNOSSOS at EMBL P14

At the European Molecular Biology Laboratory (EMBL) in Hamburg, the X-ray imaging team working at the P14 beamline on Petra III at DESY has…

031

Reposted by WEBKNOSSOS

VolumeEM @volumeem1.bsky.social · 09/03/2026

New Web Page - Volume EM Industrial Partners www.volumeem.org/industrial-p... We’re excited to introduce our newly curated Industrial Partners page, showcasing organizations recognized by the volumeEM Community as key contributors in the field.

143

WEBKNOSSOS @webknossos.org · 05/03/2026

Run pre-trained segmentation models for SEM data in WEBKNOSSOS. Test on small bounding boxes, inspect merge and split errors, and run on the full dataset once validated. View the tutorial: youtu.be/lZS2tOJYErw

011

WEBKNOSSOS @webknossos.org · 04/03/2026

Cleaning up bounding boxes just got a bit easier: multi-select (hold Ctrl/Cmd) + delete is now supported in WEBKNOSSOS.

000

WEBKNOSSOS @webknossos.org · 02/03/2026

Automatically align large volume EM datasets in WEBKNOSSOS. Run alignment and inspect results directly in the browser. Watch the tutorial: buff.ly/Edriq64

020

WEBKNOSSOS @webknossos.org · 26/02/2026

We annotated ground truth data and trained an instance segmentation model for mitochondria detection on a 140 GB mouse cortex dataset (Motta et al., 2019) in WEBKNOSSOS. See the workflow and results: medium.com/webknossos/c...

021

WEBKNOSSOS @webknossos.org · 25/02/2026

New feature 🐣 CSV export for trees! In WEBKNOSSOS, go to the Skeleton tab. Under "More actions", select "Download visible trees CSV" and check your downloads folder. Your trees are ready for analysis!

000

WEBKNOSSOS @webknossos.org · 23/02/2026

AI workflows for volume EM in WEBKNOSSOS. Align large EM datasets, run pre-trained segmentation models, train custom models on your own ground truth, and and move from small test regions to full-dataset segmentation. All workflows are now documented with step-by-step tutorials. buff.ly/LzXDNn6

020