Just published! We share an open-source workflow to measure membrane thickness from tomograms, including a tutorial with 3D visualizations. We analyze thickness variations across organelles and reflect on where to define a membrane boundary. @becklab.bsky.social #teamtomo rupress.org/jcb/article/...
November 6, 2025 at 7:38 AM
Just published! We share an open-source workflow to measure membrane thickness from tomograms, including a tutorial with 3D visualizations. We analyze thickness variations across organelles and reflect on where to define a membrane boundary. @becklab.bsky.social #teamtomo rupress.org/jcb/article/...
Diatoms – microscopic algae found almost everywhere there’s water – make up ~25% of Earth’s annual oxygen production.🌎
EMBL researchers have now found a way to easily reveal their inner structures by combining cryo-fixation with ultrastructural expansion microscopy 🔬
www.cell.com/current-biol...
EMBL researchers have now found a way to easily reveal their inner structures by combining cryo-fixation with ultrastructural expansion microscopy 🔬
www.cell.com/current-biol...
November 6, 2025 at 4:16 PM
Beautiful systematic analysis of membrane thickness inside native cells. This is a great use of both the Chlamy Dataset (bsky.app/profile/cell...) and #MemBrain segmentations (bsky.app/profile/lore...). The open-source workflow is a very helpful resource for #TeamTomo. Thanks and congrats!! 🧪 🔬
Just published! We share an open-source workflow to measure membrane thickness from tomograms, including a tutorial with 3D visualizations. We analyze thickness variations across organelles and reflect on where to define a membrane boundary. @becklab.bsky.social #teamtomo rupress.org/jcb/article/...
November 6, 2025 at 8:51 AM
Beautiful systematic analysis of membrane thickness inside native cells. This is a great use of both the Chlamy Dataset (bsky.app/profile/cell...) and #MemBrain segmentations (bsky.app/profile/lore...). The open-source workflow is a very helpful resource for #TeamTomo. Thanks and congrats!! 🧪 🔬
Hey #TeamTomo 🧪🔬, ICECREAM is getting tastier! Please give it a try on your tomograms and send us feedback so we can get the recipe just right 🍦😋
I'm pleased to announce 🍦 Icecream 🍨 v0.3!
New features include:
* Training on multiple tomograms (same training time, with linear increase in RAM) 🚀
* Logging and plotting of the loss function 📉
* The --scale option is now called --eq-weight for clarity 😉
We'd love to hear your feedback! 🙏🏽
New features include:
* Training on multiple tomograms (same training time, with linear increase in RAM) 🚀
* Logging and plotting of the loss function 📉
* The --scale option is now called --eq-weight for clarity 😉
We'd love to hear your feedback! 🙏🏽
November 6, 2025 at 8:39 AM
Hey #TeamTomo 🧪🔬, ICECREAM is getting tastier! Please give it a try on your tomograms and send us feedback so we can get the recipe just right 🍦😋
Very happy that NWO supports this major upgrade of our national EM infrastructure. It is great that this initiative got broad support all over NL, and it will EMPower fantastic science - looking forward to that!
www.uu.nl/en/news/33-m...
www.uu.nl/en/news/33-m...
33 million euro investment for national electron microscope facility EMPower
A major new national facility for electron microscopy, called EMPower, has been awarded to a consortium of Dutch universities and medical centers. EMPower aims to pave the way for major discoveries im...
www.uu.nl
November 4, 2025 at 12:33 PM
Hey #TeamTomo …would you like to try some 🍦ICECREAM!? Our @unibas.ch colleagues over at the @ivandokmanic.bsky.social lab have developed a stunningly effective tool to de-noise and de-wedge your tomograms. The contrast and details will give you brain freeze! 🍨❄️🤯
Please try, we need feedback 🧪🧶🧬🔬
Please try, we need feedback 🧪🧶🧬🔬
Our colleagues Vinith Kishore and Valentin Debarnot from the @ivandokmanic.bsky.social lab have come up with an amazing deep learning tool for denoising and filling the missing wedge in #cryoET data. I'm pleased to introduce Icecream🍧
Icecream: High-Fidelity Equivariant Cryo-Electron Tomography
Cryo-electron tomography (cryo-ET) visualizes 3D cellular architecture in near-native states. Recent deep-learning methods (CryoCARE, IsoNet, DeepDeWedge, CryoLithe) improve denoising and artifact cor...
www.biorxiv.org
October 23, 2025 at 5:57 PM
Hey #TeamTomo …would you like to try some 🍦ICECREAM!? Our @unibas.ch colleagues over at the @ivandokmanic.bsky.social lab have developed a stunningly effective tool to de-noise and de-wedge your tomograms. The contrast and details will give you brain freeze! 🍨❄️🤯
Please try, we need feedback 🧪🧶🧬🔬
Please try, we need feedback 🧪🧶🧬🔬
Icecream 🍨is open source and super easy to instaIll and run. It is already our favorite tool for denoising in the @cellarchlab.com, but it's under active development and we would love to hear your feedback!
Please give it a try and let us know:
github.com/swing-resear...
#TeamTomo
Please give it a try and let us know:
github.com/swing-resear...
#TeamTomo
GitHub - swing-research/icecream: 🍦Icecream: a self-supervised framework for cryo-ET reconstruction
🍦Icecream: a self-supervised framework for cryo-ET reconstruction - swing-research/icecream
github.com
October 23, 2025 at 11:13 AM
Icecream 🍨is open source and super easy to instaIll and run. It is already our favorite tool for denoising in the @cellarchlab.com, but it's under active development and we would love to hear your feedback!
Please give it a try and let us know:
github.com/swing-resear...
#TeamTomo
Please give it a try and let us know:
github.com/swing-resear...
#TeamTomo
Check out our preprint! With new molecular mechanisms, 140 subtomogram averages, and ~600 annotated cells under different conditions, we @embl.org were able to describe bacterial populations with in-cell #cryoET. And there’s a surprise at the end 🕵️
www.biorxiv.org/content/10.1...
#teamtomo
www.biorxiv.org/content/10.1...
#teamtomo
October 15, 2025 at 6:26 AM
Check out our preprint! With new molecular mechanisms, 140 subtomogram averages, and ~600 annotated cells under different conditions, we @embl.org were able to describe bacterial populations with in-cell #cryoET. And there’s a surprise at the end 🕵️
www.biorxiv.org/content/10.1...
#teamtomo
www.biorxiv.org/content/10.1...
#teamtomo
What happens when the cell's powerhouse gets stressed out? 💪🥵 Great visualization in this #Mitochondria #TeamTomo study! Congrats @denkenny.bsky.social @ruferbus.bsky.social & crew 🧪 🧶🧬 🔬
✨Excited that the main project of my PhD is now available as a pre-print on #bioRxiv
Here, we used #CryoET to visualise mitochondrial proteostatic stress and together with SPA #CryoEM shed light into the functional cycle of the Hsp60:10 chaperone system. #TeamTomo
🔗 www.biorxiv.org/content/10.1...
Here, we used #CryoET to visualise mitochondrial proteostatic stress and together with SPA #CryoEM shed light into the functional cycle of the Hsp60:10 chaperone system. #TeamTomo
🔗 www.biorxiv.org/content/10.1...
October 9, 2025 at 9:15 AM
What happens when the cell's powerhouse gets stressed out? 💪🥵 Great visualization in this #Mitochondria #TeamTomo study! Congrats @denkenny.bsky.social @ruferbus.bsky.social & crew 🧪 🧶🧬 🔬
✨Excited that the main project of my PhD is now available as a pre-print on #bioRxiv
Here, we used #CryoET to visualise mitochondrial proteostatic stress and together with SPA #CryoEM shed light into the functional cycle of the Hsp60:10 chaperone system. #TeamTomo
🔗 www.biorxiv.org/content/10.1...
Here, we used #CryoET to visualise mitochondrial proteostatic stress and together with SPA #CryoEM shed light into the functional cycle of the Hsp60:10 chaperone system. #TeamTomo
🔗 www.biorxiv.org/content/10.1...
October 8, 2025 at 3:59 PM
✨Excited that the main project of my PhD is now available as a pre-print on #bioRxiv
Here, we used #CryoET to visualise mitochondrial proteostatic stress and together with SPA #CryoEM shed light into the functional cycle of the Hsp60:10 chaperone system. #TeamTomo
🔗 www.biorxiv.org/content/10.1...
Here, we used #CryoET to visualise mitochondrial proteostatic stress and together with SPA #CryoEM shed light into the functional cycle of the Hsp60:10 chaperone system. #TeamTomo
🔗 www.biorxiv.org/content/10.1...
Working on #WarpTools I have the old problem of removing "bad tilts". These are views that I skipped in #etomo to get a better model...
I wrote a python code to turn the UseTilt to False in the XML files for those views and improve the tomo reconstruction.
#teamtomo
github.com/hamid13r/war...
I wrote a python code to turn the UseTilt to False in the XML files for those views and improve the tomo reconstruction.
#teamtomo
github.com/hamid13r/war...
warp_lamella_adapters/remove_bad_views.py at main · hamid13r/warp_lamella_adapters
A short optimized pipeline to get lamella tomography (with pretilt and with some tilts obscured or mistracked) to work well with Warp - hamid13r/warp_lamella_adapters
github.com
October 6, 2025 at 10:51 PM
Working on #WarpTools I have the old problem of removing "bad tilts". These are views that I skipped in #etomo to get a better model...
I wrote a python code to turn the UseTilt to False in the XML files for those views and improve the tomo reconstruction.
#teamtomo
github.com/hamid13r/war...
I wrote a python code to turn the UseTilt to False in the XML files for those views and improve the tomo reconstruction.
#teamtomo
github.com/hamid13r/war...
#TeamTomo ❄️🔬 meets #MassSpec Imaging 🧬🔬. Super cool, and great potential for EM grids with mixes of different cell types. For example -- environmental samples! @embltrec.bsky.social 🌍 🧪
Check out our new preprint on an integrated pipeline combining in situ #cryo-ET with MALDI #MSImaging for single-cell identification and classification from previously analysed EM-grids.
Link: www.biorxiv.org/content/10.1...
Link: www.biorxiv.org/content/10.1...
October 5, 2025 at 6:37 PM
#TeamTomo ❄️🔬 meets #MassSpec Imaging 🧬🔬. Super cool, and great potential for EM grids with mixes of different cell types. For example -- environmental samples! @embltrec.bsky.social 🌍 🧪
Streptophyte algae go #TeamTomo with @thanahartmann.bsky.social!
Gisela Hartmann @thanahartmann.bsky.social from @schullerjm.bsky.social lab in Marburg is telling us more about Cryo-Electron Tomography: Revealing the native cellular organization of streptophyte algae #MAdLand2025
October 2, 2025 at 1:39 PM
Streptophyte algae go #TeamTomo with @thanahartmann.bsky.social!
Thanks for highlighting our work! Here's a thread 🧵 diving into our findings and how they fit into those long-standing debates. #TeamTomo #PlantScience 🧪 🌾 🔬
bsky.app/profile/cell...
bsky.app/profile/cell...
Time for a thread!🧵 How different is the molecular organization of thylakoids in “higher” plants🌱? To find out, we teamed up with @profmattjohnson.bsky.social to dive into spinach chloroplasts with #CryoET ❄️🔬. Curious? ..Read on!
#TeamTomo #PlantScience 🧪 🧶🧬 🌾
elifesciences.org/articles/105...
1/🧵
#TeamTomo #PlantScience 🧪 🧶🧬 🌾
elifesciences.org/articles/105...
1/🧵
September 29, 2025 at 8:07 AM
Thanks for highlighting our work! Here's a thread 🧵 diving into our findings and how they fit into those long-standing debates. #TeamTomo #PlantScience 🧪 🌾 🔬
bsky.app/profile/cell...
bsky.app/profile/cell...
But there’s a curious loose end to this story. Scientists have been looking at PSII organization in thylakoids for over 50 years (including some really stunning freeze fracture 🔬😍). Sometimes PSII looks randomly oriented, and other times it forms extended 2D crystalline arrays in the membrane 💠
9/🧵
9/🧵
September 27, 2025 at 5:13 PM
Time for a thread!🧵 How different is the molecular organization of thylakoids in “higher” plants🌱? To find out, we teamed up with @profmattjohnson.bsky.social to dive into spinach chloroplasts with #CryoET ❄️🔬. Curious? ..Read on!
#TeamTomo #PlantScience 🧪 🧶🧬 🌾
elifesciences.org/articles/105...
1/🧵
#TeamTomo #PlantScience 🧪 🧶🧬 🌾
elifesciences.org/articles/105...
1/🧵
September 25, 2025 at 6:00 PM
Time for a thread!🧵 How different is the molecular organization of thylakoids in “higher” plants🌱? To find out, we teamed up with @profmattjohnson.bsky.social to dive into spinach chloroplasts with #CryoET ❄️🔬. Curious? ..Read on!
#TeamTomo #PlantScience 🧪 🧶🧬 🌾
elifesciences.org/articles/105...
1/🧵
#TeamTomo #PlantScience 🧪 🧶🧬 🌾
elifesciences.org/articles/105...
1/🧵
Last but not least, HUGE thanks🙏 to all our collaborators (especially the very patient @profmattjohnson.bsky.social) & everyone who helped along the (long long) way!🤗
#TeamTomo @drlornamalone.bsky.social @dtegunov.bsky.social
@mpibiochem.bsky.social @pioneercampus.bsky.social @biozentrum.unibas.ch
#TeamTomo @drlornamalone.bsky.social @dtegunov.bsky.social
@mpibiochem.bsky.social @pioneercampus.bsky.social @biozentrum.unibas.ch
September 25, 2025 at 7:14 PM
Last but not least, HUGE thanks🙏 to all our collaborators (especially the very patient @profmattjohnson.bsky.social) & everyone who helped along the (long long) way!🤗
#TeamTomo @drlornamalone.bsky.social @dtegunov.bsky.social
@mpibiochem.bsky.social @pioneercampus.bsky.social @biozentrum.unibas.ch
#TeamTomo @drlornamalone.bsky.social @dtegunov.bsky.social
@mpibiochem.bsky.social @pioneercampus.bsky.social @biozentrum.unibas.ch
Huntingtin binds and bundles F-actin!
Thrilled to team up with the Humbert (Sorbonne Université) and Song (KAIST) labs on this discovery.
We had a blast doing cryo-ET on this unexpected complex — and now so many new questions lie ahead!
#TeamTomo #CryoET #HTT #actin
doi.org/10.1126/scia...
Thrilled to team up with the Humbert (Sorbonne Université) and Song (KAIST) labs on this discovery.
We had a blast doing cryo-ET on this unexpected complex — and now so many new questions lie ahead!
#TeamTomo #CryoET #HTT #actin
doi.org/10.1126/scia...
September 25, 2025 at 3:01 PM
Huntingtin binds and bundles F-actin!
Thrilled to team up with the Humbert (Sorbonne Université) and Song (KAIST) labs on this discovery.
We had a blast doing cryo-ET on this unexpected complex — and now so many new questions lie ahead!
#TeamTomo #CryoET #HTT #actin
doi.org/10.1126/scia...
Thrilled to team up with the Humbert (Sorbonne Université) and Song (KAIST) labs on this discovery.
We had a blast doing cryo-ET on this unexpected complex — and now so many new questions lie ahead!
#TeamTomo #CryoET #HTT #actin
doi.org/10.1126/scia...
They Let Me Put Coffee In A CT Scanner!
YouTube video by James Hoffmann
www.youtube.com
September 23, 2025 at 9:55 PM
Huntingtin protein bound to actin filaments. I didn’t know it could do that! Nice one @schurlab.bsky.social and friends! 🧪🧶🧬 #TeamTomo
Cryo-ET visualization of HTT bound to F-actin, highlighted in the yellow square on the left.
On the right, a detailed zoom-in view of the molecular model of the HTT/F-actin complex is shown.
On the right, a detailed zoom-in view of the molecular model of the HTT/F-actin complex is shown.
September 22, 2025 at 4:25 PM
Huntingtin protein bound to actin filaments. I didn’t know it could do that! Nice one @schurlab.bsky.social and friends! 🧪🧶🧬 #TeamTomo
A molecular-resolution look into the near-native architecture of the spinach chloroplast🌱. This one was a long time in the oven, but we're happy to finally share our "version of record". What long-standing debates did we settle? Check back for a short thread🧵 on Monday. #TeamTomo #PlantScience 🧪🧶🧬🔬🌾
🌱 Using ‘compelling’ methods, including #CryoET, researchers mapped spinach thylakoid membranes at single-molecule precision, revealing how photosynthetic complexes are organised and settling long-standing debates on chloroplast architecture.
buff.ly/j3TSIkn
buff.ly/j3TSIkn
September 20, 2025 at 7:24 PM
A molecular-resolution look into the near-native architecture of the spinach chloroplast🌱. This one was a long time in the oven, but we're happy to finally share our "version of record". What long-standing debates did we settle? Check back for a short thread🧵 on Monday. #TeamTomo #PlantScience 🧪🧶🧬🔬🌾
Thanks Alister! That Feynman catchphrase is certainly words to live by for #TeamTomo. I actually used to intro my talks with it. But the trick is in the full quote-- these "easy" observations rely on making our microscopes (and tools for analysis) more powerful. Thanks for your help with #MemBrain 🤗
September 20, 2025 at 8:18 PM
Thanks Alister! That Feynman catchphrase is certainly words to live by for #TeamTomo. I actually used to intro my talks with it. But the trick is in the full quote-- these "easy" observations rely on making our microscopes (and tools for analysis) more powerful. Thanks for your help with #MemBrain 🤗
Coming up next week: the third Dutch Structural Biology meeting! Now in Delft, on Sept 26. See program here: nvbmb.kncv.nl/biology-2025 with #teamtomo #cryoEM #nmrchat simulations and more (looks like)
Organized by the #NVBMB (associated with KNCV)
Organized by the #NVBMB (associated with KNCV)
Dutch Structural Biology Meeting 2025 - NVBMB
nvbmb.kncv.nl
September 18, 2025 at 9:02 PM
Coming up next week: the third Dutch Structural Biology meeting! Now in Delft, on Sept 26. See program here: nvbmb.kncv.nl/biology-2025 with #teamtomo #cryoEM #nmrchat simulations and more (looks like)
Organized by the #NVBMB (associated with KNCV)
Organized by the #NVBMB (associated with KNCV)
obviously teamtomo is perfect and no mistakes have ever been made 👀
September 16, 2025 at 7:17 PM
obviously teamtomo is perfect and no mistakes have ever been made 👀