iiinova — where your digital self keeps evolving

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Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · 23/09/2026

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

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Jan-Hendrik Müller @kolibril13.bsky.social · 25/08/2026

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!

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Aafke Gros @aafkegros.bsky.social · 24/08/2026

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! 🔬🎉

youtube.com

Split & Animate Microscopy Volumes in Blender | Microscopy Nodes 3.1.2

YouTube video by Aafke Gros

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Aafke Gros @aafkegros.bsky.social · 24/07/2026

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...

A FIB-SEM plankton visualization where the top shows only the volumetric data of the chromosomes, and the bottom a normally sliced region of the cell.

A fluorescence microscopy dataset where a region has been reloaded to be much higher resolution

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Jan-Hendrik Müller @kolibril13.bsky.social · 21/07/2026

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...

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Victoria Deneke @vdeneke.bsky.social · 22/05/2026

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! 🧵👇

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Eugene Katrukha 🇺🇦 @ekatrukha.bsky.social · 21/05/2026

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.

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Eugene Katrukha 🇺🇦 @ekatrukha.bsky.social · 23/04/2026

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).

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Jacques Lucke @jacqueslucke.bsky.social · 24/04/2026

#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

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Martin Weigert @maweigert.bsky.social · 02/03/2026

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

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Zwicker Group @zwickergroup.bsky.social · 15/12/2025

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...

arxiv.org

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...

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Pierre Haas @lepuslapis.bsky.social · 07/03/2025

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

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Arseny Kapoulkine @zeux.io · 08/12/2025

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

meshoptimizer.org

🐇 meshoptimizer v1.0

Mesh optimization library that makes meshes smaller and faster to render

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Eugene Katrukha 🇺🇦 @ekatrukha.bsky.social · 17/11/2025

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)

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Ben Gallusser @bengallusser.bsky.social · 20/11/2025

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 🤖

imagej.net

TrackMate Trackastra

Trackastra integration in TrackMate.

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Constantin Pape @cppape.bsky.social · 17/10/2025

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....

SynapseNet is a deep learning based software tool that automates the segmentation of vesicles, mitochondria, synaptic compartments, and the active zone. This is visualized in three panels. On the left, a section of an electron tomogram with a synaptic compartment densely filled with vesicles, which appear as round structures with dark boundary and light body in the image, is shwon. The top right panel shows the segmentation result of vesicles, visualized by masks with an individual color per vesicle and outlines for the segmented compartment (red) and active zone (blue). The bottom right panels shows a 3D rendering of the segmentation with vesicles shown as yellow spheres.

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ilastik-team.bsky.social @ilastik-team.bsky.social · 09/10/2025

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/🧵

Large images have to be broken into tiles both for training and inference with neural networks. The tile predictions then need to be merged to produce the final volume prediction.

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Aafke Gros @aafkegros.bsky.social · 24/09/2025

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!

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Anna Foix @afoix.bsky.social · 23/09/2025

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)

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Eugene Katrukha 🇺🇦 @ekatrukha.bsky.social · 19/09/2025

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

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Aafke Gros @aafkegros.bsky.social · 19/09/2025

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

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Aafke Gros @aafkegros.bsky.social · 19/09/2025

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

youtu.be

Microscopy Nodes: handling large biological volumes — Blender Conference 2025

YouTube video by Blender

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Susan Cox @micoxscopy.bsky.social · 12/08/2025

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...

biorxiv.org

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...

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Talley Lambert @talley.codes · 05/07/2025

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! 🙏

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Andy Moore @aaandmoore.bsky.social · 22/04/2025

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...

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Aafke Gros @aafkegros.bsky.social · 23/05/2025

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...

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ilastik-team.bsky.social @ilastik-team.bsky.social · 16/05/2025

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

ilastik.org

ilastik - Download

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hollypbird.bsky.social @hollypbird.bsky.social · 03/04/2025

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.

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Nemo Andrea @cursed-tubule.bsky.social · 07/03/2025

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...

youtube.com

Procedural Microtubule | Blender 3.1 Geometry Nodes

YouTube video by Nemo Andrea

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ANeves @arneves.bsky.social · 19/02/2025

My PhD work in the Köhler lab showing an involvement of a synaptonemal complex component in crossover regulation independently of synapsis is now published in NAR! 🎊 #meiosis #crossovers #C.elegans 🧬 Check it out here: academic.oup.com/nar/article/...

academic.oup.com

Crossovers are regulated by a conserved and disordered synaptonemal complex domain

Abstract. During meiosis, the number and distribution of crossovers (COs) must be precisely regulated through CO assurance and interference to prevent chro

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Eugene Katrukha 🇺🇦 @ekatrukha.bsky.social · 06/02/2025

Together with Christian Tischer, 3D rendering of multi-res microscopy data was added to MoBIE FIJI plugin using #BigVolumeViewer. Check any remote datasets (like @dudinlab.bsky.social maps of protists using ExM) in the highest quality. For full details read forum.image.sc/t/mobie-plus...

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Jean-Yves Tinevez @jytinevez.bsky.social · 30/01/2025

10 - Featured extension: Mastodon-Blender Offers a bridge from Mastodon to Blender to create high quality 3D rendering of lineages and cell tracks over time: (Tracking data of phallusia mammillata embryogenesis by Guignard et a. (2020). doi.org/10.1126/scie...)

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Aafke Gros @aafkegros.bsky.social · 30/01/2025

Now out in PLOS CB: Spherical Texture extraction! doi.org/10.1371/jour... This method quantifies the intensity distribution in microscopy objects, and is implemented parameter-free in @ilastik-team.bsky.social object classification! We show applications in cells, C. elegans and Drosophila! 😁

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Aafke Gros @aafkegros.bsky.social · 15/01/2025

Microscopy Nodes is now up on bioRxiv! 🚀 This is a Blender extension that seamlessly integrates and visualizes 3D microscopy data (TIF & @zarr.dev). High-quality volume rendering for anyone, in both EM and fluorescence, regardless of computational expertise! 🔬 www.biorxiv.org/content/10.1...

FIB-SEM dataset visualized with Microscopy Nodes, data from Mocaer et al 2023

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Aafke Gros @aafkegros.bsky.social · 10/12/2024

In honor of the first ever #MicroscopyNodes stickers arriving, I'm assembling my purse of open source bio(image) projects 😋. Which ones am I missing?😸

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Aafke Gros @aafkegros.bsky.social · 20/11/2024

Messing around with the new #Blender 4.3 volume scatter modes with #microscopynodes, while at the #OME #Zarr hackathon! 😁🤩 Great info and work on the upcoming features of Zarr here :D Transforms, collections, and more! 🙏

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Aafke Gros @aafkegros.bsky.social · 18/11/2024

Wow! Amazing video! Happy to see that Microscopy Nodes is useful to you 😋 I love that your render shows all the versatility of rendering microscopy data in Blender, that you don't often have access to in microscopy-specific implementations 😁🙏

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Aafke Gros @aafkegros.bsky.social · 21/10/2024

Microscopy Nodes 2.0 is out! This includes a new channel interface and OME-Zarr support! 🔬🎉 www.youtube.com/watch?v=ybQc...

youtube.com

Installing and using Microscopy Nodes in Blender

YouTube video by Oane Gros

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