Ben Engel
@cellarchlab.com
cellarchlab.com Univ. of Basel Biozentrum🇨🇭. Exploring molecular architecture inside cells with #CryoEM #TeamTomo. Plants and algae in a changing climate. ❄🔬 OF 🌿 4THE 🌍!
Pinned
Ben Engel
@cellarchlab.com
· Jan 6
Towards community-driven visual proteomics! Excited to finally share this large-scale curated & annotated dataset of 1829 high-quality #cryoET tomograms of the little green alga that just keeps giving— Chlamydomonas! 🧪🧶🧬🌾🌊🌍
Preprint📜: www.biorxiv.org/content/10.1...
A short thread🧵👇
Preprint📜: www.biorxiv.org/content/10.1...
A short thread🧵👇
Reposted by Ben Engel
New Title Alert: Icecream- a self-supervised framework for cryo-ET reconstruction that integrates equivariance principles from modern imaging theory into a deep-learning architecture.
Learn more here: buff.ly/bdepEUm
#SBGrid #SBGridSoftware #StructuralBiology
Learn more here: buff.ly/bdepEUm
#SBGrid #SBGridSoftware #StructuralBiology
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
buff.ly
November 19, 2025 at 5:03 PM
New Title Alert: Icecream- a self-supervised framework for cryo-ET reconstruction that integrates equivariance principles from modern imaging theory into a deep-learning architecture.
Learn more here: buff.ly/bdepEUm
#SBGrid #SBGridSoftware #StructuralBiology
Learn more here: buff.ly/bdepEUm
#SBGrid #SBGridSoftware #StructuralBiology
Reposted by Ben Engel
Prohibitins aren’t hanging out just anywhere in the membrane — they prefer the 💁♀️💎✨VIP section💅🪩🥂
Lab all-star @mmedina300kv.bsky.social maps these microdomains using cryo-ET + surface morphometrics.
s/o to #teamtomo #cryoET co-authors
@hamid13r.bsky.social
@attychang.bsky.social
@baradlab.com
Lab all-star @mmedina300kv.bsky.social maps these microdomains using cryo-ET + surface morphometrics.
s/o to #teamtomo #cryoET co-authors
@hamid13r.bsky.social
@attychang.bsky.social
@baradlab.com
Prohibitin complexes associate with unique membrane microdomains in cells https://www.biorxiv.org/content/10.1101/2025.11.14.688579v1
November 17, 2025 at 12:22 AM
Prohibitins aren’t hanging out just anywhere in the membrane — they prefer the 💁♀️💎✨VIP section💅🪩🥂
Lab all-star @mmedina300kv.bsky.social maps these microdomains using cryo-ET + surface morphometrics.
s/o to #teamtomo #cryoET co-authors
@hamid13r.bsky.social
@attychang.bsky.social
@baradlab.com
Lab all-star @mmedina300kv.bsky.social maps these microdomains using cryo-ET + surface morphometrics.
s/o to #teamtomo #cryoET co-authors
@hamid13r.bsky.social
@attychang.bsky.social
@baradlab.com
Very pretty #SciArt 🧪 🎨 render of Asgard chromatin 🧬 (determined by the @dodonova-sveta.bsky.social lab). Nice one Leonora! 👩🔬👩🎨
November 11, 2025 at 10:12 PM
Very pretty #SciArt 🧪 🎨 render of Asgard chromatin 🧬 (determined by the @dodonova-sveta.bsky.social lab). Nice one Leonora! 👩🔬👩🎨
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!! 🧪 🔬
Reposted by Ben Engel
Always happy to see the #ChlamyDataset put to good use 😉
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 8:00 AM
Always happy to see the #ChlamyDataset put to good use 😉
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 🍦😋
Reposted by Ben Engel
Very thorough work that applies cryo-ET to measure bilayer thickness. Surprisingly, the missing wedge is not a big problem!
Glushkova, Böhm, & Beck @maxplanck.de develop a publicly available computational method to measure the thickness of biological membranes in cryo-electron tomograms. Analysis of algae & human cells reveals systematic membrane thickness variations within & across organelles rupress.org/jcb/article/...
November 5, 2025 at 1:00 PM
Very thorough work that applies cryo-ET to measure bilayer thickness. Surprisingly, the missing wedge is not a big problem!
Check out #DinoSphere 🦖🪩 -- Early Career Researchers sharing their latest insights into dinoflagellate biology. Online and free. Tune in! 👩🔬📺
#ProtistsOnSky 🧪🌊 🌍 🔬
#ProtistsOnSky 🧪🌊 🌍 🔬
We’re back with the next DinoSphere Online Seminar!
Join us on Nov 4th, we're hosting:
Edmée Royen (ULiège) - Symbiodinium
Nicolas dos Santos Pacheco (Cambridge) - Perkinsids
📅 Tue, Nov 4 - 4 PM CET/3 PM GMT
💻 Zoom link: sites.google.com/view/dinosphere
Please spread the word!
#protistonsky
Join us on Nov 4th, we're hosting:
Edmée Royen (ULiège) - Symbiodinium
Nicolas dos Santos Pacheco (Cambridge) - Perkinsids
📅 Tue, Nov 4 - 4 PM CET/3 PM GMT
💻 Zoom link: sites.google.com/view/dinosphere
Please spread the word!
#protistonsky
October 29, 2025 at 8:04 AM
Check out #DinoSphere 🦖🪩 -- Early Career Researchers sharing their latest insights into dinoflagellate biology. Online and free. Tune in! 👩🔬📺
#ProtistsOnSky 🧪🌊 🌍 🔬
#ProtistsOnSky 🧪🌊 🌍 🔬
Intriguing structures of Asgard hypernucleosomes in open and closed conformations provide a glimpse into the evolution of chromatin from our closest prokaryotic relatives. Bold and eye-opening work by the @dodonova-sveta.bsky.social lab! Also great visualization 🧪👩🔬🎨 #CryoEM #ArchaeaSky
Lab’s first paper is out!! We show the first structures of #Asgard #chromatin by #cryo-EM 🧬❄️
Asgard histones form closed and open hypernucleosomes. Closed are conserved across #Archaea, while open resemble eukaryotic H3–H4 octasomes and are Asgard-specific. More here: www.cell.com/molecular-ce...
Asgard histones form closed and open hypernucleosomes. Closed are conserved across #Archaea, while open resemble eukaryotic H3–H4 octasomes and are Asgard-specific. More here: www.cell.com/molecular-ce...
October 29, 2025 at 4:12 AM
Intriguing structures of Asgard hypernucleosomes in open and closed conformations provide a glimpse into the evolution of chromatin from our closest prokaryotic relatives. Bold and eye-opening work by the @dodonova-sveta.bsky.social lab! Also great visualization 🧪👩🔬🎨 #CryoEM #ArchaeaSky
REMINDER! One week left to apply for what (in my humble and somewhat biased opinion) is one of the best academic jobs on the planet! Come join our vibrant and collaborative community here at the @biozentrum.unibas.ch @unibas.ch 🧪
EXCITING NEWS!! We're searching for a new professor colleague at the Biozentrum🇨🇭. Ideal candidates are exploring novel biological questions with structure, biophysics, or high-resolution imaging. 🧪 🧶🧬 🔬
The call closes Nov 3. Please get in touch if you would like more information. Come join us! 👩🔬🤓
The call closes Nov 3. Please get in touch if you would like more information. Come join us! 👩🔬🤓
October 27, 2025 at 12:52 PM
REMINDER! One week left to apply for what (in my humble and somewhat biased opinion) is one of the best academic jobs on the planet! Come join our vibrant and collaborative community here at the @biozentrum.unibas.ch @unibas.ch 🧪
Reposted by Ben Engel
Last Friday (17th), we had an amazing first Young Swiss Tomo meeting in Bern, organized with Elda Bauda, Zanetta Kechagia, and @leonieanton.bsky.social!
Over 70 people from 🇨🇭 gathered to talk about cryo-electron tomography 🔬.
Huge thanks to the DCI for making the event possible! See you next year! 👋
Over 70 people from 🇨🇭 gathered to talk about cryo-electron tomography 🔬.
Huge thanks to the DCI for making the event possible! See you next year! 👋
October 19, 2025 at 9:16 AM
Last Friday (17th), we had an amazing first Young Swiss Tomo meeting in Bern, organized with Elda Bauda, Zanetta Kechagia, and @leonieanton.bsky.social!
Over 70 people from 🇨🇭 gathered to talk about cryo-electron tomography 🔬.
Huge thanks to the DCI for making the event possible! See you next year! 👋
Over 70 people from 🇨🇭 gathered to talk about cryo-electron tomography 🔬.
Huge thanks to the DCI for making the event possible! See you next year! 👋
A class like no other!! From #AI structure hallucination 🤖 to #CryoEM structure reality 🔬 by @biozentrum.unibas.ch @unibas.ch undergraduate students👩🔬👩🎓 in just a few weeks!
One of their creations is this beautiful flower-shaped tetrameric pore 🌼, a brand new member of the #ProteinCosmos 🧶🧬 🧪
One of their creations is this beautiful flower-shaped tetrameric pore 🌼, a brand new member of the #ProteinCosmos 🧶🧬 🧪
October 26, 2025 at 1:48 PM
A class like no other!! From #AI structure hallucination 🤖 to #CryoEM structure reality 🔬 by @biozentrum.unibas.ch @unibas.ch undergraduate students👩🔬👩🎓 in just a few weeks!
One of their creations is this beautiful flower-shaped tetrameric pore 🌼, a brand new member of the #ProteinCosmos 🧶🧬 🧪
One of their creations is this beautiful flower-shaped tetrameric pore 🌼, a brand new member of the #ProteinCosmos 🧶🧬 🧪
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 🧪🧶🧬🔬
Reposted by Ben Engel
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
Reposted by Ben Engel
Sounds like fun to deposit 140 subtomogram averages 😳
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 11:07 AM
Sounds like fun to deposit 140 subtomogram averages 😳
So, we all know that VIPP1 (the Very Important Protein in Plants) is the "photosynthetic ESCRT-III", required for the biogenesis and maintenance of light-harvesting thylakoids. But what about ESCRT-II, you say? ...Meet VIA1! Congrats @mayankdu.bsky.social on your lab's first paper! #PlantScience 🧪 🌾
Hot off the press, first PI paper 🎉. Reporting a novel protein (VIA1) involved in thylakoid membrane biogenesis. VIA1 (similar to ESCRT-II) and bind to chloroplast ESCRT-III (VIPP1). Showing a direct role of VIPP1 in thylakoid biogenesis.
@cp-cellreports.bsky.social
tinyurl.com/msrepdna
@cp-cellreports.bsky.social
tinyurl.com/msrepdna
October 14, 2025 at 12:30 PM
So, we all know that VIPP1 (the Very Important Protein in Plants) is the "photosynthetic ESCRT-III", required for the biogenesis and maintenance of light-harvesting thylakoids. But what about ESCRT-II, you say? ...Meet VIA1! Congrats @mayankdu.bsky.social on your lab's first paper! #PlantScience 🧪 🌾
Let’s stare into the far red 🏮. A stunning tour-de-force of high-resolution #CryoEM by Gio, Bill, & company reveals how the machinery of photosynthesis redshifts itself so cyanobacteria can live on far red light, deep in the cracks of rocks or under microbial mats. #PlantScience 🧪 🧶🧬 🌾 🔬 🌍
Have you ever looked at the night sky and wondered if there’s a chlorophyll f in the reaction centre of Photosystem I from far-red light adapted cyanobacteria? 🦠
Well, we did (don’t judge) and the work that followed is now out as a First Release in @science.org
www.science.org/doi/10.1126/...
Well, we did (don’t judge) and the work that followed is now out as a First Release in @science.org
www.science.org/doi/10.1126/...
Locating the missing chlorophylls f in far-red photosystem I
The discovery of chlorophyll f-containing photosystems, with their long-wavelength photochemistry, represented a distinct, low-energy paradigm for oxygenic photosynthesis. Structural studies on chloro...
www.science.org
October 13, 2025 at 9:08 PM
Let’s stare into the far red 🏮. A stunning tour-de-force of high-resolution #CryoEM by Gio, Bill, & company reveals how the machinery of photosynthesis redshifts itself so cyanobacteria can live on far red light, deep in the cracks of rocks or under microbial mats. #PlantScience 🧪 🧶🧬 🌾 🔬 🌍
The KEY🔑 to regulating Rubisco phase separation in the Chlamydomonas algal pyrenoid. Beautiful work by Shan He, @mjonikas.bsky.social, and friends. #PhaseSeparation #CO2 #PlantScience 🧪 🧶🧬 🌾 🌍
Algal pyrenoids—condensates that mediate ~1/3 of Earth’s CO2 fixation—change size and number as cells divide. Our data suggest a simple control mechanism: a kinase that continuously ejects material from the condensate! ☀️🌍🔬💧 #Biophysics #Photosynthesis
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
October 12, 2025 at 9:26 PM
The KEY🔑 to regulating Rubisco phase separation in the Chlamydomonas algal pyrenoid. Beautiful work by Shan He, @mjonikas.bsky.social, and friends. #PhaseSeparation #CO2 #PlantScience 🧪 🧶🧬 🌾 🌍
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 🧪 🧶🧬 🔬
Hellooooo beautiful!😍 #CryoEM #ArchaeaSky 🧪
Out in Science Advances: Our #cryoEM structure of HFTV1, a virus infecting the halophile #archaea. *First full atomic structure (containing all structural proteins) of any tailed virus!* Congrats and thanks to all co-authors and our fantastic collaborators! www.science.org/doi/10.1126/...
Cryo-EM resolves the structure of the archaeal dsDNA virus HFTV1 from head to tail
This structure of an archaeal tailed virus (arTV) provides detailed insights into arTV assembly and infection mechanisms.
www.science.org
October 6, 2025 at 3:57 PM
Hellooooo beautiful!😍 #CryoEM #ArchaeaSky 🧪
#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 🌍 🧪
Reposted by Ben Engel
So much fun to host @edwardmarcotte.bsky.social at the @biozentrum.unibas.ch and introduce him to the @cellarchlab.com, thanks for a wonderful Discovery Seminar!!
October 4, 2025 at 8:56 AM
So much fun to host @edwardmarcotte.bsky.social at the @biozentrum.unibas.ch and introduce him to the @cellarchlab.com, thanks for a wonderful Discovery Seminar!!
Reposted by Ben Engel
A place with fantastic colleagues, excellent facilities, a stimulating scientific environment, and a very international and vibrant city - it's got it all!
EXCITING NEWS!! We're searching for a new professor colleague at the Biozentrum🇨🇭. Ideal candidates are exploring novel biological questions with structure, biophysics, or high-resolution imaging. 🧪 🧶🧬 🔬
The call closes Nov 3. Please get in touch if you would like more information. Come join us! 👩🔬🤓
The call closes Nov 3. Please get in touch if you would like more information. Come join us! 👩🔬🤓
October 1, 2025 at 8:33 AM
A place with fantastic colleagues, excellent facilities, a stimulating scientific environment, and a very international and vibrant city - it's got it all!
Reposted by Ben Engel
Biocenter is THE BEST!
Assistant/Associate Professor in Structural Biology, Biophysics or Biological Imaging
www.biozentrum.unibas.ch/open-positio...
#biozentrum #University #Basel #Professor #Structural #Biology #Biophysics #Biological #Imaging
www.biozentrum.unibas.ch/open-positio...
#biozentrum #University #Basel #Professor #Structural #Biology #Biophysics #Biological #Imaging
September 30, 2025 at 4:41 PM
Biocenter is THE BEST!
Reposted by Ben Engel
Come join us in Basel! @biozentrum.unibas.ch is an amazing place to start your group.
Assistant/Associate Professor in Structural Biology, Biophysics or Biological Imaging
www.biozentrum.unibas.ch/open-positio...
#biozentrum #University #Basel #Professor #Structural #Biology #Biophysics #Biological #Imaging
www.biozentrum.unibas.ch/open-positio...
#biozentrum #University #Basel #Professor #Structural #Biology #Biophysics #Biological #Imaging
September 29, 2025 at 6:35 PM
Come join us in Basel! @biozentrum.unibas.ch is an amazing place to start your group.