What if any dataset, any size, any number of dimensions, opened in a browser tab from a link? 🔬🧪💻 Luxar is out today: write it in Python, share it as a link, explore it in any browser. Open source. 🧵 @biohub.org Preprint: doi.org/10.5281/zen... Code: github.com/royerlab/luxar

A scene that I wanted to see for the longest time: Putting a tomographic dataset into a handcrafted physics simlution. And finally, it's possible! 😍 With the help of Lars from @algebraic-ug.bsky.social and Microscopy Nodes @aafkegros.bsky.social we can now render this cell animation in Blender!

Split and animate separate subregions of your microscopy volumes with Microscopy Nodes! www.youtube.com/watch?v=7K-i... You can make your 3D cells sort to their classified locations, explode/reassemble your segmented tissue - and everything in full volumetric space! 🔬🎉

Split & Animate Microscopy Volumes in Blender | Microscopy Nodes 3.1.2

YouTube video by Aafke Gros

youtube.com

Microscopy Nodes 3.1 is out for Blender 5.2! 🎉 This has cool new features for conditional masking, working with even larger data (regional upscaling), and data manipulation! Watch the new youtube tutorials that explain the features: www.youtube.com/playlist?lis...

In the render below, you can see the organels of a marine plankton, measure by an electron microscope. Blender 5.2 is already incredible, but with with the latest release of Microscopy Nodes by @aafkegros.bsky.social, cell rendering is pretty like never before. extensions.blender.org/add-ons/micr...

How do sperm and egg fuse? Surprisingly, we still don’t fully know… Our field has uncovered many pieces of the fertilization puzzle, but not how they fit together. We identify ✨ SPARK ✨ - a conserved sperm complex that couples sperm-egg binding to fusion. tinyurl.com/34cm4xat Read on! 🧵👇

New release of #BigVolumeBrowser (0.1.1) adds support for (multiscale) OME-Zarr (thanks to libraries from @bogovicj.bsky.social, Stefan Hahmann, Vladimir Ulman). And midi gizmo navigation (from @herrsaalfeld.bsky.social ), shown below.

New release of #BigTrace is out (0.9.0): finally, IJ macro concurrency is fixed (hopefully), added groovy scripting, moved to its own Fiji listed update site, and it has proper ROI transparency rendering (below).

#GeometryNodes will have a new Sample Sound Frequencies node in Blender 5.2. It allows creating animations and simulations based on audio data without having to use non-procedural workarounds. #b3d #devfund

Excited to share our new paper (CVPR 2026 🚀): "MuViT: Multi-Resolution Vision Transformers for Learning Across Scales in Microscopy" which enables local predictions to use global context. Great work led by @albertdm.bsky.social & another fun collab w @gioelelamanno.bsky.social! @scadsai.bsky.social

Since more than a decade, our group has been exploring chemically active droplets, which are exciting since their size can be controlled. Yet, we still do not fully understand this control even in the simplest models. Until a new preprint (arxiv.org/abs/2512.02542) spearheaded by postdoc Guido...

Size control guidelines for chemically active droplets

Biological cells and synthetic analogues use liquid-liquid phase separation to dynamically compartmentalize their environment for various applications. In many cases, multiple droplets need to coexist...

arxiv.org

New #preprint: "Euler buckling on curved surfaces" arxiv.org/abs/2503.04303 @zhaoshh.bsky.social and I ask the question that Euler left open: How does an elastic line buckle within a (general) curved surface? @mpipks.bsky.social @mpi-cbg.de @csbdresden.bsky.social

After nine years of development, meshoptimizer has reached its first major version, 1.0! This release focuses on improvements in clusterization and simplification as well as stabilization. Here's a release announcement with more details on past, present and future; please RT! meshoptimizer.org/v1

Turns out, there are fully opened LIDAR point scans of the whole Netherlands surface available geotiles.nl With up to 25 cm. It was hard not to load our building and around it into #bigvolumebrowser (22 M points + Fire LUT for height)

Finally, the first public release of #BigVolumeBrowser, so after teasers, you can try it yourself. For details, please check the announcement post (1/2) forum.image.sc/t/bigvolumeb...

BigVolumeBrowser: a new 3D multi volume/mesh/point clould (SMLM) data viewer

Hello everyone, I’d like to share with you another 3D viewer for FIJI, BigVolumeBrowser (full documentation link). It‘s a first initial public release, so there is still space for improvements. Le...

forum.image.sc

Trackastra is part of the brand-new TrackMate v8. It is the first deep-learning-based ("AI") drop-in replacement for TrackMate's regular LAP-Track algorithm. Tracks out of the box for many types of datasets (bacteria, fluorescent nuclei, phase contrast cell culture etc), zero parameters to tune 🤖

TrackMate Trackastra

Trackastra integration in TrackMate.

imagej.net

Jean-Yves Tinevez@jytinevez.bsky.social · 11mo ago

With an image with a proper background >.<

Are you studying synapses in electron microscopy? Tired of annotating vesicles? We have the tool for you! SynapseNet implements automatic segmentation and analysis of vesicles and other synaptic structures and has now been published: www.molbiolcell.org/doi/full/10....

Segment large images without tiling artifacts: sharing our work that should have been presented at ICCV in 2 weeks - the brilliant first author Elena can’t go because of visa issues. The paper: arxiv.org/abs/2503.19545 1/🧵

Automatic filament tracing in 3D data is now only a few clicks (or one macro) away! In the amazing #BigTrace FIJI plugin by @ekatrukha.bsky.social 🤩 My workflow will be to autotrace and then manually correct the autotraces, reducing the time for our tracing significantly!

Eugene Katrukha 🇺🇦@ekatrukha.bsky.social · last yr.

New release of #BigTrace plugin is out. Together with @aafkegros.bsky.social from Simone Köhler group we added a fully automatic tracing mode. + more macro functions and bug fixes github.com/ekatrukha/Bi...

Happy to share that ShapeEmbed has been accepted at @neuripsconf.bsky.social 🎉 SE is self-supervised framework to encode 2D contours from microscopy & natural images into a latent representation invariant to translation, scaling, rotation, reflection & point indexing 📄 arxiv.org/pdf/2507.01009 (1/N)

A cell finding its way through the matrix, imaged with @joycemeiri.bsky.social on LLS.

Amazing to see real-world medical applications of blender volume handling! 🤩🤩🤩

jordan@jordan.matelsky.com · last yr.

so proud to share @jhuapl.bsky.social neuroscience research at #blenderconference2025 @blender.org ❤️ also shoutout to #microscopynodes by @aafkegros.bsky.social, here's to awesome new collabs born at blendercon!!!

I gave a talk at Blender Conference yesterday, showing how biological volumes work, and how to visualize them in Blender 😋 youtu.be/WPajSWX730o?... #bcon25

Microscopy Nodes: handling large biological volumes — Blender Conference 2025

YouTube video by Blender

youtu.be

How do you quantify cell structures which are deformed between different observations? Our preprint shows how to perform Simultaneous QUAntification of Structure and Structural Heterogeneity (SQUASSH) on 3D fluorescence microscopy data. (1/5) www.biorxiv.org/content/10.1...

Extracting biological structure and heterogeneity from the nano to the macro scale

Fluorescence microscopy is an essential tool in biology. It has revealed great variability at multiple scales, in macromolecular complexes, cells, and organisms. Understanding this variability will re...

biorxiv.org

it was already fun to look around the documentation for cmap (cmap-docs.readthedocs.io) but @grosoane.bsky.social just added a very cool feature to toggle between color vision deficiencies. Watch your perceptually uniform color maps gain some kinks 😂 as a mild deutan myself, I appreciate it! 🙏

Happy to officially introduce FilaBuster - a strategy for rapid, light-mediated intermediate filament disassembly. Compatible with multiple IF types, modular in design, and precise enough to induce localized filament disassembly in live cells. www.biorxiv.org/content/10.1...

In the context of our @reviewcommons.org revision process, I'm happy to announce Microscopy Nodes v2.2.0! This packs lots of new fun features, including new color management 🌈, clearer transparency handling 🫥, custom default settings 🔧 and more! Preprint at doi.org/10.1101/2025...

New stable ilastik version 1.4.1 at www.ilastik.org/download! Release Highlights: - Support for OME-zarr (v0.4) - New workflow - Trainable Domain Adaptation - New object features based on Spherical Harmonics Feature, contributed by @grosoane.bsky.social. - Native support for Apple Silicon

So excited to be a collaborator on this! We used @grosoane.bsky.social #microscopynodes to import tomo data to Blender before passing to Sensu for the beautiful animation.

Leah Lavery@helloleahlavery.bsky.social · 2y ago

So thrilled to unveil the Krios 5 Cryo-TEM for studying cellular structures and molecular interactions. Thank you to the many, many teammates that made this possible. Watch the video! Watch the more & sign up for virtual event on May 14: ter.li/ueeqfs www.linkedin.com/posts/thermo...

It would only be appropriate to post about the #geometrynodes #microtubule here too. For a full introduction, I have prepared the world's least professional youtube video. www.youtube.com/watch?v=AYUy...

Procedural Microtubule | Blender 3.1 Geometry Nodes

YouTube video by Nemo Andrea

youtube.com