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!

💎 Oldy but goldy: version history in WEBKNOSSOS. Every annotation keeps a full history. Made a mistake hours ago? Open the history and restore any earlier state. Your work is never lost. #WEBKNOSSOS

🌟Enhancement🌟 You can now add an optional segmentation layer to your animations. Select it next to your color layer in the Create Animation dialog, and it will appear in your rendered video.Try it at webknossos.org!

Maximum intensity projection in WEBKNOSSOS 🐣 Select a bounding box, choose which layers to render, fine-tune the ray marching step, and enable depth-correct rendering for accurate 3D rendering. Try it on webknossos.org!

💎 Oldy but goldy: the AI quick-select tool. Click a structure or drag a box and WEBKNOSSOS segments it for you. Set the prediction depth to label many sections at once, in 2D or 3D. #WEBKNOSSOS

💎 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

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/neuroa… #neuroanatomy #connectomics #WEBKNOSSOS

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

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/cre…

💎 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

💎 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

💎 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

💎 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.

💎 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.

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.

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

“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. Read more: home.webknossos.org/blog/tea…

“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. Read more: home.webknossos.org/blog/tea…

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

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.