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
Reposted by Ben Engel
A super detailed protocol + video on Cryo-ExM - Cryo-Expansion Microscopy, led by the labs of our former postdocs @marinelap.bsky.social & @ebertiaux.bsky.social.
Clear, practical, and very useful for anyone doing nanoscale imaging 🚀 app.jove.com/t/68595/expa...
Clear, practical, and very useful for anyone doing nanoscale imaging 🚀 app.jove.com/t/68595/expa...
December 25, 2025 at 1:41 PM
A super detailed protocol + video on Cryo-ExM - Cryo-Expansion Microscopy, led by the labs of our former postdocs @marinelap.bsky.social & @ebertiaux.bsky.social.
Clear, practical, and very useful for anyone doing nanoscale imaging 🚀 app.jove.com/t/68595/expa...
Clear, practical, and very useful for anyone doing nanoscale imaging 🚀 app.jove.com/t/68595/expa...
Reposted by Ben Engel
Final version is out! Our large-scale cryo-ET dataset 🔬 of Chlamydomonas reinhardtii 🦠 is now published in @cp-molcell.bsky.social
Huge collaborative effort! So glad to see the community already using it to develop new resources & tools.
Check it out here: shorturl.at/z4i4c
#CryoEM #CryoET
Huge collaborative effort! So glad to see the community already using it to develop new resources & tools.
Check it out here: shorturl.at/z4i4c
#CryoEM #CryoET
December 19, 2025 at 4:45 PM
Final version is out! Our large-scale cryo-ET dataset 🔬 of Chlamydomonas reinhardtii 🦠 is now published in @cp-molcell.bsky.social
Huge collaborative effort! So glad to see the community already using it to develop new resources & tools.
Check it out here: shorturl.at/z4i4c
#CryoEM #CryoET
Huge collaborative effort! So glad to see the community already using it to develop new resources & tools.
Check it out here: shorturl.at/z4i4c
#CryoEM #CryoET
Reposted by Ben Engel
Happy to see IsoNet2 performing so well on the #ChlamyDataset EMPIAR-11830. Congrats to the authors really great work.
However, I have to say this tomogram looks amazing because the lamella is way too thin (~50 nm) and not vitreous! 🫠
www.biorxiv.org/content/10.6...
However, I have to say this tomogram looks amazing because the lamella is way too thin (~50 nm) and not vitreous! 🫠
www.biorxiv.org/content/10.6...
December 12, 2025 at 5:18 PM
Happy to see IsoNet2 performing so well on the #ChlamyDataset EMPIAR-11830. Congrats to the authors really great work.
However, I have to say this tomogram looks amazing because the lamella is way too thin (~50 nm) and not vitreous! 🫠
www.biorxiv.org/content/10.6...
However, I have to say this tomogram looks amazing because the lamella is way too thin (~50 nm) and not vitreous! 🫠
www.biorxiv.org/content/10.6...
Reposted by Ben Engel
Holy cow the Zhou lab at UCLA is cooking with Isonet 2 - www.biorxiv.org/content/10.6...
Averaging-free direct visualization of ribosome translational state! #teamtomo #cryoet
Averaging-free direct visualization of ribosome translational state! #teamtomo #cryoet
December 12, 2025 at 3:53 PM
Holy cow the Zhou lab at UCLA is cooking with Isonet 2 - www.biorxiv.org/content/10.6...
Averaging-free direct visualization of ribosome translational state! #teamtomo #cryoet
Averaging-free direct visualization of ribosome translational state! #teamtomo #cryoet
Reposted by Ben Engel
Postdoc opportunity with Michel Goedert and myself to work on #cryoEM/#cryoET structures of #amyloids. Feel free to email me with any questions you might have.
mrc.tal.net/vx/mobile-0/...
mrc.tal.net/vx/mobile-0/...
Postdoctoral Scientist - Neurobiology - Dr Michel Goedert - LMB 2752 - Medical Research Council
Location: Cambridge. Vacancy: Postdoctoral Scientist - Neurobiology - Dr Michel Goedert - LMB 2752. Closing Date: 04/01/2026, 23:55
mrc.tal.net
December 10, 2025 at 2:28 PM
Postdoc opportunity with Michel Goedert and myself to work on #cryoEM/#cryoET structures of #amyloids. Feel free to email me with any questions you might have.
mrc.tal.net/vx/mobile-0/...
mrc.tal.net/vx/mobile-0/...
Reposted by Ben Engel
🥳 Our new paper on C2CD3 is out in @plosbiology.org
With the labs of @cellarchlab.com , @chgenoud.bsky.social , and @stearnslab.bsky.social , we revealed the mammalian centriole Distal Ring architecture by combining #UExM and in situ #CryoET.
Big congrats to @ebertiaux.bsky.social and all involved.
With the labs of @cellarchlab.com , @chgenoud.bsky.social , and @stearnslab.bsky.social , we revealed the mammalian centriole Distal Ring architecture by combining #UExM and in situ #CryoET.
Big congrats to @ebertiaux.bsky.social and all involved.
How does C2CD3 contribute to distal appendage formation in centrioles? @centriolelab.bsky.social show that C2CD3 acts as a central architectural organizer of the distal #centriole, bridging the luminal distal ring complex & peripheral appendage sites @plosbiology.org 🧪 plos.io/496XZuH
December 10, 2025 at 12:36 PM
🥳 Our new paper on C2CD3 is out in @plosbiology.org
With the labs of @cellarchlab.com , @chgenoud.bsky.social , and @stearnslab.bsky.social , we revealed the mammalian centriole Distal Ring architecture by combining #UExM and in situ #CryoET.
Big congrats to @ebertiaux.bsky.social and all involved.
With the labs of @cellarchlab.com , @chgenoud.bsky.social , and @stearnslab.bsky.social , we revealed the mammalian centriole Distal Ring architecture by combining #UExM and in situ #CryoET.
Big congrats to @ebertiaux.bsky.social and all involved.
Reposted by Ben Engel
Thrilled to share that my postdoc paper has just been a published in @plosbiology.org !
Thank you to all co-authors, and a special thanks to Paul and Virginie @centriolelab.bsky.social for their support throughout this work.
Proud of what we achieved together!
journals.plos.org/plosbiology/...
Thank you to all co-authors, and a special thanks to Paul and Virginie @centriolelab.bsky.social for their support throughout this work.
Proud of what we achieved together!
journals.plos.org/plosbiology/...
The luminal ring protein C2CD3 acts as a radial in-to-out organizer of the distal centriole and appendages
The centriolar protein C2CD3 has been suggested to be crucial for distal appendage formation in centrioles, but its precise mechanistic role remains unclear. Using a combination of ultrastructure expa...
journals.plos.org
December 10, 2025 at 8:29 AM
Thrilled to share that my postdoc paper has just been a published in @plosbiology.org !
Thank you to all co-authors, and a special thanks to Paul and Virginie @centriolelab.bsky.social for their support throughout this work.
Proud of what we achieved together!
journals.plos.org/plosbiology/...
Thank you to all co-authors, and a special thanks to Paul and Virginie @centriolelab.bsky.social for their support throughout this work.
Proud of what we achieved together!
journals.plos.org/plosbiology/...
Happy to share our fun team-up with @centriolelab.bsky.social & @stearnslab.bsky.social to reveal the architecture of the mammalian centriole’s Distal Ring 🛟. Very cool multiscale integration of #UExM 📏🔬with #CryoET ❄️🔬. Congrats to @ebertiaux.bsky.social & @computingcaitie.bsky.social #TeamTomo 🧪
How does C2CD3 contribute to distal appendage formation in centrioles? @centriolelab.bsky.social show that C2CD3 acts as a central architectural organizer of the distal #centriole, bridging the luminal distal ring complex & peripheral appendage sites @plosbiology.org 🧪 plos.io/496XZuH
December 10, 2025 at 11:02 AM
Happy to share our fun team-up with @centriolelab.bsky.social & @stearnslab.bsky.social to reveal the architecture of the mammalian centriole’s Distal Ring 🛟. Very cool multiscale integration of #UExM 📏🔬with #CryoET ❄️🔬. Congrats to @ebertiaux.bsky.social & @computingcaitie.bsky.social #TeamTomo 🧪
Reposted by Ben Engel
What an honor to see @attychang.bsky.social’s work featured in @jcb.org The Year in Cell Biology 2025 collection! Even more special that it coincides with my first #cellbio2025 conference 🙂
s/o to co-authors @baradlab.com @hamid13r.bsky.social @zidlab.bsky.social
#teamtomo #cellbio25
s/o to co-authors @baradlab.com @hamid13r.bsky.social @zidlab.bsky.social
#teamtomo #cellbio25
@attychang.bsky.social, @nanigrotjahn.bsky.social et al. show that cytoplasmic #ribosomes on #mitochondria alter the local membrane environment for protein import. rupress.org/jcb/article/...
📕 From The Year In Cell Biology: rupress.org/jcb/collecti...
#CellBio2025
📕 From The Year In Cell Biology: rupress.org/jcb/collecti...
#CellBio2025
December 7, 2025 at 8:10 PM
What an honor to see @attychang.bsky.social’s work featured in @jcb.org The Year in Cell Biology 2025 collection! Even more special that it coincides with my first #cellbio2025 conference 🙂
s/o to co-authors @baradlab.com @hamid13r.bsky.social @zidlab.bsky.social
#teamtomo #cellbio25
s/o to co-authors @baradlab.com @hamid13r.bsky.social @zidlab.bsky.social
#teamtomo #cellbio25
Reposted by Ben Engel
CryoET of microbes inside an animal organ? Yes it’s possible! Check out our new preprint showing how we did it! What an amazing collaboration with amazing scientists who made this possible!
Nanoscale imaging of native symbiotic animal tissue using amultimodal large volume imaging pipeline for cryo-electrontomography https://www.biorxiv.org/content/10.1101/2025.11.30.691379v1
December 1, 2025 at 4:35 AM
CryoET of microbes inside an animal organ? Yes it’s possible! Check out our new preprint showing how we did it! What an amazing collaboration with amazing scientists who made this possible!
Great talk (and work 🧪 ) by @computingcaitie.bsky.social from @biozentrum.unibas.ch about exploring multiciliated cells with a complementary trio of structural techniques! Looking forward to sharing the preprint. Thanks for the fab collab @centriolelab.bsky.social @stearnslab.bsky.social #TeamTomo
Next up @computingcaitie.bsky.social from @cellarchlab.com marvels us with in situ structural biology of mammalian motile cilia base- power of #cryoET with #XL-MS & #UExM! Stunning cataloguing of MIPs in different axial positions & cilia types, filamentous actin in action. #UKCilia2025 /3
November 25, 2025 at 7:30 PM
Great talk (and work 🧪 ) by @computingcaitie.bsky.social from @biozentrum.unibas.ch about exploring multiciliated cells with a complementary trio of structural techniques! Looking forward to sharing the preprint. Thanks for the fab collab @centriolelab.bsky.social @stearnslab.bsky.social #TeamTomo
Reposted by Ben Engel
Each such discovery is a game changer for our understanding of eukaryote evolution, and this paper is no exception. Meet Solarion, which displays yet again novel types of subcellular structures. Congrats to all authors on a fascinating story. #protistsonsky
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Rare microbial relict sheds light on an ancient eukaryotic supergroup - Nature
The discovery of an unusual protist named Solarion arienae, which has a mitochondrial genome with some intriguing features, provides insight into the early radiation of eukaryotic groups.
www.nature.com
November 21, 2025 at 9:30 AM
Each such discovery is a game changer for our understanding of eukaryote evolution, and this paper is no exception. Meet Solarion, which displays yet again novel types of subcellular structures. Congrats to all authors on a fascinating story. #protistsonsky
www.nature.com/articles/s41...
www.nature.com/articles/s41...
It was a joy to spend some time with you Philippe! Thanks for visiting and sharing your cool IFT Train research with us! 🚂🚂🚂🧪
Great time yesterday visiting @biozentrum.unibas.ch many thanks to Alexey Baldin for invitation & organisation, to all lab members of @cellarchlab.com for the cilia debates and of the Spang lab for trafficking and... aging discussions! Impressive building... and nice lights at the train station 😍
November 21, 2025 at 4:05 PM
It was a joy to spend some time with you Philippe! Thanks for visiting and sharing your cool IFT Train research with us! 🚂🚂🚂🧪
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! 👋