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!

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! 🤩🤩🤩

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

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...

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.

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...

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/...

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...

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...)

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! 😁

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...

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?😸

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! 🙏

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 😁🙏

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