Aafke Gros
@aafkegros.bsky.social
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
she/her | IPA: ˈafkə ɡrɔs
Pinned
Aafke Gros
@aafkegros.bsky.social
· Sep 19
Microscopy Nodes: handling large biological volumes — Blender Conference 2025
YouTube video by Blender
youtu.be
I gave a talk at Blender Conference yesterday, showing how biological volumes work, and how to visualize them in Blender 😋 youtu.be/WPajSWX730o?... #bcon25
Reposted by Aafke Gros
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....
www.molbiolcell.org/doi/full/10....
October 17, 2025 at 11:09 AM
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....
www.molbiolcell.org/doi/full/10....
Reposted by Aafke Gros
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/🧵
The paper: arxiv.org/abs/2503.19545 1/🧵
October 9, 2025 at 12:56 PM
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/🧵
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!
My workflow will be to autotrace and then manually correct the autotraces, reducing the time for our tracing significantly!
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...
September 24, 2025 at 12:05 PM
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!
My workflow will be to autotrace and then manually correct the autotraces, reducing the time for our tracing significantly!
Reposted by Aafke Gros
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)
📄 arxiv.org/pdf/2507.01009 (1/N)
September 23, 2025 at 8:32 AM
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)
📄 arxiv.org/pdf/2507.01009 (1/N)
Reposted by Aafke Gros
A cell finding its way through the matrix, imaged with @joycemeiri.bsky.social on LLS.
September 19, 2025 at 10:38 AM
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! 🤩🤩🤩
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!!!
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
September 19, 2025 at 12:44 PM
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
Microscopy Nodes: handling large biological volumes — Blender Conference 2025
YouTube video by Blender
youtu.be
September 19, 2025 at 7:35 AM
I gave a talk at Blender Conference yesterday, showing how biological volumes work, and how to visualize them in Blender 😋 youtu.be/WPajSWX730o?... #bcon25
Reposted by Aafke Gros
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...
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
August 12, 2025 at 4:20 PM
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...
www.biorxiv.org/content/10.1...
Reposted by Aafke Gros
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! 🙏
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! 🙏
July 5, 2025 at 8:28 PM
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! 🙏
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! 🙏
Reposted by Aafke Gros
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...
www.biorxiv.org/content/10.1...
April 22, 2025 at 1:02 AM
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...
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...
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...
May 23, 2025 at 1:13 PM
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...
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...
Reposted by Aafke Gros
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
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
May 16, 2025 at 10:45 AM
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
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
Reposted by Aafke Gros
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.
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...
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
April 3, 2025 at 4:50 PM
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.
Reposted by Aafke Gros
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...
www.youtube.com/watch?v=AYUy...
Procedural Microtubule | Blender 3.1 Geometry Nodes
YouTube video by Nemo Andrea
www.youtube.com
March 7, 2025 at 10:04 PM
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...
www.youtube.com/watch?v=AYUy...
Reposted by Aafke Gros
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/...
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
February 19, 2025 at 9:29 AM
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/...
Check it out here: academic.oup.com/nar/article/...
Reposted by Aafke Gros
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...
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...
February 6, 2025 at 8:55 PM
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...
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...
Reposted by Aafke Gros
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...)
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...)
January 30, 2025 at 4:44 PM
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...)
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! 😁
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! 😁
January 30, 2025 at 10:11 AM
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! 😁
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...
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...
January 15, 2025 at 1:39 PM
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...
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?😸
December 10, 2024 at 9:23 AM
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! 🙏
Great info and work on the upcoming features of Zarr here :D Transforms, collections, and more! 🙏
November 20, 2024 at 10:33 AM
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! 🙏
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 😁🙏
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 😁🙏
Next up, microscopy nodes for Blender, made by @grosoane.bsky.social, which lets you import microscopy images as efficient voxel representations for generating animations (ie below, from EMPIAR-10982). I've had a lot of fun playing around with it the last couple of weeks. github.com/oanegros/Mic...
November 18, 2024 at 3:53 PM
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 😁🙏
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...
www.youtube.com/watch?v=ybQc...
Installing and using Microscopy Nodes in Blender
YouTube video by Oane Gros
www.youtube.com
October 21, 2024 at 8:28 AM
Microscopy Nodes 2.0 is out! This includes a new channel interface and OME-Zarr support! 🔬🎉
www.youtube.com/watch?v=ybQc...
www.youtube.com/watch?v=ybQc...