banner
aafkegros.bsky.social
Aafke Gros
@aafkegros.bsky.social
750 followers 280 following 29 posts
Check out Microscopy Nodes for handling microscopy data in Blender! Now loading .tif and OME-Zarr with big volume support :) she/her | IPA: ˈafkə ɡrɔs
Posts Media Videos Starter Packs
Pinned
aafkegros.bsky.social
Aafke Gros @aafkegros.bsky.social · 19d
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
2 13 53
aafkegros.bsky.social
Aafke Gros @aafkegros.bsky.social · 14d
Ah right, I have also seen some of the napari solution! I think this in general makes a lot of sense, and I'm still looking into how to make these kinds of volume interactions as easy in Blender as they are in the more scientific software, such as BigTrace and Napari 😅😋
1 1
aafkegros.bsky.social
Aafke Gros @aafkegros.bsky.social · 14d
This is separate from Blender, built on imglib2 in java (same framework as bigDataViewer, so also related to bigWarp), and for bigtrace all implemented by @ekatrukha.bsky.social

I think the smart thing it does for annotation is to extract the brightest point under the mouse as targeted point
1 1 3
aafkegros.bsky.social
Aafke Gros @aafkegros.bsky.social · 14d
This is the cool part of BigTrace, where this also has extensive semimanual and manual modes, while seeing your data in 3D. So this way, you can use the same engine to delete and fix traces.

Additionally i still want to make some automatic flags based on time info, but that will be more custom.
1 2
aafkegros.bsky.social
Aafke Gros @aafkegros.bsky.social · 14d
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!
ekatrukha.bsky.social
Eugene Katrukha 🇺🇦 @ekatrukha.bsky.social · 14d
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...
1 4 16
Reposted by Aafke Gros
afoix.bsky.social
Anna Foix @afoix.bsky.social · 15d
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)
3 23 60
Reposted by Aafke Gros
ekatrukha.bsky.social
Eugene Katrukha 🇺🇦 @ekatrukha.bsky.social · 19d
A cell finding its way through the matrix, imaged with @joycemeiri.bsky.social on LLS.
1 12 33
aafkegros.bsky.social
Aafke Gros @aafkegros.bsky.social · 19d
Amazing to see real-world medical applications of blender volume handling! 🤩🤩🤩
jordan.matelsky.com
jordan @jordan.matelsky.com · 19d
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!!!
Blending brains: Tales from the neuro department — Blender Conference 2025
YouTube video by Blender
youtu.be
1 6
aafkegros.bsky.social
Aafke Gros @aafkegros.bsky.social · 19d
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
2 13 53
aafkegros.bsky.social
Aafke Gros @aafkegros.bsky.social · Aug 27
I think it can be very useful to give a 'diorama' feel to a render and highlight certain complexity! But probably mostly for artistic purposes
1 1
Reposted by Aafke Gros
micoxscopy.bsky.social
Susan Cox @micoxscopy.bsky.social · Aug 12
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...
www.biorxiv.org
1 7 28
Reposted by Aafke Gros
talley.codes
Talley Lambert @talley.codes · Jul 5
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! 🙏
9 29
Reposted by Aafke Gros
aaandmoore.bsky.social
Andy Moore @aaandmoore.bsky.social · Apr 22
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...
2 36 120
aafkegros.bsky.social
Aafke Gros @aafkegros.bsky.social · May 23
This is accompanied by a new set of tutorials showing exactly how you can start making beautiful microscopy visualizations in @blender.org!
Following along is also easy with the example OME-Zarr @openmicroscopy.org datasets 😄
Find the tutorials here: www.youtube.com/playlist?lis...
7 30
aafkegros.bsky.social
Aafke Gros @aafkegros.bsky.social · May 23
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...
2 31 88
Reposted by Aafke Gros
ilastik-team.bsky.social
ilastik-team.bsky.social @ilastik-team.bsky.social · May 16
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 - Download
www.ilastik.org
1 3 11
Reposted by Aafke Gros
hollypbird.bsky.social
hollypbird.bsky.social @hollypbird.bsky.social · Apr 3
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.
helloleahlavery.bsky.social
Leah Lavery @helloleahlavery.bsky.social · Apr 2
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...
Introducing the Krios 5 Cryo-Transmission Electron Microscope | Thermo Fisher Scientific
Today, we introduce the Krios 5 Cryo-Transmission Electron Microscope, which provides atomic-level insights to help scientists study how cells, proteins and viruses work. Its enhanced optics and new A...
www.linkedin.com
1 7
Reposted by Aafke Gros
cursed-tubule.bsky.social
Nemo Andrea @cursed-tubule.bsky.social · Mar 7
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
www.youtube.com
3 19
Reposted by Aafke Gros
arneves.bsky.social
ANeves @arneves.bsky.social · Feb 19
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/...
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
academic.oup.com
2 9
Reposted by Aafke Gros
ekatrukha.bsky.social
Eugene Katrukha 🇺🇦 @ekatrukha.bsky.social · Feb 6
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...
23 65
Reposted by Aafke Gros
jytinevez.bsky.social
Jean-Yves Tinevez @jytinevez.bsky.social · Jan 30
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...)
1 3 17
aafkegros.bsky.social
Aafke Gros @aafkegros.bsky.social · Jan 30
And it also works in 2D 😁 Here we extract a circular projection instead of a spherical, and apply a 1D Fourier transform.
Here we can see how the channel distributions all align in the projection after we optically activate Rac1 in one part of the cell. 💡
With @jpassmore.bsky.social , Lukas Kapitein
2
aafkegros.bsky.social
Aafke Gros @aafkegros.bsky.social · Jan 30
With the integration into the accessible toolkit ilastik (@ilastik-team.bsky.social) you can very easily include this in a quickly and interactively retrainable classification algorithm.
We show this for classification of meiotic zones in C. elegans :) 🪱

For the nerds there's also a Python API 😉
1 3
aafkegros.bsky.social
Aafke Gros @aafkegros.bsky.social · Jan 30
Quantifying distribution of intensity can be very helpful in many biological systems. For example, in D. melanogaster data, we extract a peak for the level of embryonic patterning in development. 🪰
In collaboration with
@ottilie.bsky.social, @timothyfuqua.bsky.social, @justinmcrocker.bsky.social
1 2 6
aafkegros.bsky.social
Aafke Gros @aafkegros.bsky.social · Jan 30
We then use spherical harmonics decomposition to quantify the variance in the spherical signal per angular wavelength.
This gives us a metric that shows how detailed the features in the spherical map are, giving a rotation-invariant quantification of distribution.
1 2
aafkegros.bsky.social
Aafke Gros @aafkegros.bsky.social · Jan 30
To quantify a segmented microscopy object, we project this to a spherical mean map.

This video is made with @blender3d.bsky.social geometry nodes and Microscopy Nodes, allowing the microscopy and method illustration in the same video :D
1 4