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
This one was quite the journey! The paper describing the #ChlamyDataset is finally out and on the cover of Mol Cell!
This beautiful rendering made by co-author @jessheebner.bsky.social and Holly Peterson shows an instance of mitochondrial fission found in the dataset 😍
[Maybe long thread ahead]
This beautiful rendering made by co-author @jessheebner.bsky.social and Holly Peterson shows an instance of mitochondrial fission found in the dataset 😍
[Maybe long thread ahead]
The #ChlamyDataset is on the cover of @cp-molcell.bsky.social 🖼️🥰!
Read @lifeonthewedge.bsky.social's great thread🧵 for the inside scoop🍨 on all the #TeamTomo developments already made possible since these 1829 tomos hit EMPIAR 🧪 🧶🧬
For more, here's the old preprint thread:
bsky.app/profile/cell...
Read @lifeonthewedge.bsky.social's great thread🧵 for the inside scoop🍨 on all the #TeamTomo developments already made possible since these 1829 tomos hit EMPIAR 🧪 🧶🧬
For more, here's the old preprint thread:
bsky.app/profile/cell...
Reposted by Ben Engel
I'm so happy to have gotten the opportunity to work on this project and I'm SO excited that they selected our image for the cover!
This one was quite the journey! The paper describing the #ChlamyDataset is finally out and on the cover of Mol Cell!
This beautiful rendering made by co-author @jessheebner.bsky.social and Holly Peterson shows an instance of mitochondrial fission found in the dataset 😍
[Maybe long thread ahead]
This beautiful rendering made by co-author @jessheebner.bsky.social and Holly Peterson shows an instance of mitochondrial fission found in the dataset 😍
[Maybe long thread ahead]
January 9, 2026 at 7:20 PM
I'm so happy to have gotten the opportunity to work on this project and I'm SO excited that they selected our image for the cover!
Reposted by Ben Engel
What a great example of collaborative science enabled by people sharing things early on. Well done @lifeonthewedge.bsky.social and others!
This one was quite the journey! The paper describing the #ChlamyDataset is finally out and on the cover of Mol Cell!
This beautiful rendering made by co-author @jessheebner.bsky.social and Holly Peterson shows an instance of mitochondrial fission found in the dataset 😍
[Maybe long thread ahead]
This beautiful rendering made by co-author @jessheebner.bsky.social and Holly Peterson shows an instance of mitochondrial fission found in the dataset 😍
[Maybe long thread ahead]
January 9, 2026 at 9:28 PM
What a great example of collaborative science enabled by people sharing things early on. Well done @lifeonthewedge.bsky.social and others!
The #ChlamyDataset is on the cover of @cp-molcell.bsky.social 🖼️🥰!
Read @lifeonthewedge.bsky.social's great thread🧵 for the inside scoop🍨 on all the #TeamTomo developments already made possible since these 1829 tomos hit EMPIAR 🧪 🧶🧬
For more, here's the old preprint thread:
bsky.app/profile/cell...
Read @lifeonthewedge.bsky.social's great thread🧵 for the inside scoop🍨 on all the #TeamTomo developments already made possible since these 1829 tomos hit EMPIAR 🧪 🧶🧬
For more, here's the old preprint thread:
bsky.app/profile/cell...
This one was quite the journey! The paper describing the #ChlamyDataset is finally out and on the cover of Mol Cell!
This beautiful rendering made by co-author @jessheebner.bsky.social and Holly Peterson shows an instance of mitochondrial fission found in the dataset 😍
[Maybe long thread ahead]
This beautiful rendering made by co-author @jessheebner.bsky.social and Holly Peterson shows an instance of mitochondrial fission found in the dataset 😍
[Maybe long thread ahead]
January 9, 2026 at 7:49 PM
The #ChlamyDataset is on the cover of @cp-molcell.bsky.social 🖼️🥰!
Read @lifeonthewedge.bsky.social's great thread🧵 for the inside scoop🍨 on all the #TeamTomo developments already made possible since these 1829 tomos hit EMPIAR 🧪 🧶🧬
For more, here's the old preprint thread:
bsky.app/profile/cell...
Read @lifeonthewedge.bsky.social's great thread🧵 for the inside scoop🍨 on all the #TeamTomo developments already made possible since these 1829 tomos hit EMPIAR 🧪 🧶🧬
For more, here's the old preprint thread:
bsky.app/profile/cell...
Reposted by Ben Engel
#teamtomo gets another quantitative cell biology tool!
We extend our Surface Morphometrics pipeline to measure membrane thickness.
Alongside many biological findings, we show that our 3D measurements closely match in vitro vesicle measurements from 2D EM (collab w/Neal Waxham and Fred Heberle).
We extend our Surface Morphometrics pipeline to measure membrane thickness.
Alongside many biological findings, we show that our 3D measurements closely match in vitro vesicle measurements from 2D EM (collab w/Neal Waxham and Fred Heberle).
Medina, Chang et al. of the @nanigrotjahn.bsky.social lab introduce a new method based on the Surface Morphometrics pipeline to measure global and local thicknesses of organellar #membranes from cellular cryo-electron tomography data. rupress.org/jcb/article/...
#CryoET
#CryoET
January 6, 2026 at 1:51 AM
#teamtomo gets another quantitative cell biology tool!
We extend our Surface Morphometrics pipeline to measure membrane thickness.
Alongside many biological findings, we show that our 3D measurements closely match in vitro vesicle measurements from 2D EM (collab w/Neal Waxham and Fred Heberle).
We extend our Surface Morphometrics pipeline to measure membrane thickness.
Alongside many biological findings, we show that our 3D measurements closely match in vitro vesicle measurements from 2D EM (collab w/Neal Waxham and Fred Heberle).
ER-associated single-capped vaults are surprising and really cool!🤩 Some even contain ribosomes. Vault function is still mysterious but a role in protein quality control seems plausible.
Also great to see Dicty in the #TeamTomo spotlight! #ProtistsOnSky @kgeissler.bsky.social @becklab.bsky.social 🧪
Also great to see Dicty in the #TeamTomo spotlight! #ProtistsOnSky @kgeissler.bsky.social @becklab.bsky.social 🧪
December 28, 2025 at 12:54 PM
ER-associated single-capped vaults are surprising and really cool!🤩 Some even contain ribosomes. Vault function is still mysterious but a role in protein quality control seems plausible.
Also great to see Dicty in the #TeamTomo spotlight! #ProtistsOnSky @kgeissler.bsky.social @becklab.bsky.social 🧪
Also great to see Dicty in the #TeamTomo spotlight! #ProtistsOnSky @kgeissler.bsky.social @becklab.bsky.social 🧪
Reposted by Ben Engel
Another #notTHECover unfortunately.
But this gorgeous, Tron-like vibe, drawn by the amazing @munafomarzia.bsky.social for our recent #ExM work with @gautamdey.bsky.social & @centriolelab.bsky.social will still be printed out in the lab.
Read here: www.cell.com/cell/fulltex...
But this gorgeous, Tron-like vibe, drawn by the amazing @munafomarzia.bsky.social for our recent #ExM work with @gautamdey.bsky.social & @centriolelab.bsky.social will still be printed out in the lab.
Read here: www.cell.com/cell/fulltex...
December 26, 2025 at 11:53 AM
Another #notTHECover unfortunately.
But this gorgeous, Tron-like vibe, drawn by the amazing @munafomarzia.bsky.social for our recent #ExM work with @gautamdey.bsky.social & @centriolelab.bsky.social will still be printed out in the lab.
Read here: www.cell.com/cell/fulltex...
But this gorgeous, Tron-like vibe, drawn by the amazing @munafomarzia.bsky.social for our recent #ExM work with @gautamdey.bsky.social & @centriolelab.bsky.social will still be printed out in the lab.
Read here: www.cell.com/cell/fulltex...
December 28, 2025 at 4:37 AM
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!! 🧪 🔬