Philippe Van der Stappen
@phaips.vd.st
Rubisco phase separation + Cryo-ET
PhD @ Engel & Hondele Lab Biozentrum Basel 𝗖𝗛
#TeamTomo
PhD @ Engel & Hondele Lab Biozentrum Basel 𝗖𝗛
#TeamTomo
Pinned
Welcome to TomoGuide
A step-by-step Cryo-ET guide
tomoguide.github.io
Hey #TeamTomo,
Ever been in need of a tutorial about the fundamentals of cryo-electron tomography? From preprocessing raw frames to high-res subtomogram averaging?
That's why @florentwaltz.bsky.social and I made this website!
tomoguide.github.io
Follow the thread 1 /🧵
#CryoET #CryoEM 🔬🧪
Ever been in need of a tutorial about the fundamentals of cryo-electron tomography? From preprocessing raw frames to high-res subtomogram averaging?
That's why @florentwaltz.bsky.social and I made this website!
tomoguide.github.io
Follow the thread 1 /🧵
#CryoET #CryoEM 🔬🧪
Icecream for extra crispy tomos 🥶
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 12:23 PM
Icecream for extra crispy tomos 🥶
Reposted by Philippe Van der Stappen
#Proteomic analysis of the #pyrenoid‐traversing membranes of #Chlamydomonas #reinhardtii reveals novel components
📖 nph.onlinelibrary.wiley.com/doi/10.1111/...
by Franklin et al.
@mjonikas.bsky.social @ericfranklin.bsky.social @WileyPlantSci
📖 nph.onlinelibrary.wiley.com/doi/10.1111/...
by Franklin et al.
@mjonikas.bsky.social @ericfranklin.bsky.social @WileyPlantSci
October 23, 2025 at 1:45 AM
#Proteomic analysis of the #pyrenoid‐traversing membranes of #Chlamydomonas #reinhardtii reveals novel components
📖 nph.onlinelibrary.wiley.com/doi/10.1111/...
by Franklin et al.
@mjonikas.bsky.social @ericfranklin.bsky.social @WileyPlantSci
📖 nph.onlinelibrary.wiley.com/doi/10.1111/...
by Franklin et al.
@mjonikas.bsky.social @ericfranklin.bsky.social @WileyPlantSci
Reposted by Philippe Van der Stappen
Apply for our Master of Science in Physics of Life – training in cutting-edge research at the interface of physics, mathematics, engineering and life sciences. Scholarships available. Application deadline: 30 November. More: www.biozentrum.unibas.ch/education/de...
@biozentrum.unibas.ch @unibas.ch
@biozentrum.unibas.ch @unibas.ch
October 17, 2025 at 9:22 AM
Apply for our Master of Science in Physics of Life – training in cutting-edge research at the interface of physics, mathematics, engineering and life sciences. Scholarships available. Application deadline: 30 November. More: www.biozentrum.unibas.ch/education/de...
@biozentrum.unibas.ch @unibas.ch
@biozentrum.unibas.ch @unibas.ch
Reposted by Philippe Van der Stappen
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 1:22 PM
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...
Reposted by Philippe Van der Stappen
Reposted by Philippe Van der Stappen
Another record month for bioRxiv - and further evidence the pandemic spike+dip was just that and growth continues. Thanks to all involved and that includes 🫵
October 1, 2025 at 3:51 PM
Another record month for bioRxiv - and further evidence the pandemic spike+dip was just that and growth continues. Thanks to all involved and that includes 🫵
Reposted by Philippe Van der Stappen
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 2:58 PM
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
Reposted by Philippe Van der Stappen
CryoET is a particularly brutal area for combining a spectacular public success with hidden heroic failure!
September 16, 2025 at 2:32 PM
CryoET is a particularly brutal area for combining a spectacular public success with hidden heroic failure!
Reposted by Philippe Van der Stappen
Authors concluded that this study “demonstrates that following current climate policies will not only overshoot the 1.5-°C limit of the Paris Agreement by a wide margin but also may prohibit returning to it thereafter.” Wishful thinking is not a realistic strategy for future generations.
⬇️ ⬇️ ⬇️
⬇️ ⬇️ ⬇️
September 4, 2025 at 8:43 AM
Authors concluded that this study “demonstrates that following current climate policies will not only overshoot the 1.5-°C limit of the Paris Agreement by a wide margin but also may prohibit returning to it thereafter.” Wishful thinking is not a realistic strategy for future generations.
⬇️ ⬇️ ⬇️
⬇️ ⬇️ ⬇️
Reposted by Philippe Van der Stappen
🧪 The University of Basel is setting up a new endowed professorship in #ClimateBiophysics at the @biozentrum.unibas.ch, funded by the Georg H. Endress Foundation. This new professorship strengthens climate research @unibas.ch. www.biozentrum.unibas.ch/news/detail/...
New endowed professorship strengthens climate research at the University of Basel
The University of Basel is setting up a new endowed professorship at the Biozentrum to make fundamental discoveries at the interface between biophysics and climate-relevant environmental biology. This...
www.biozentrum.unibas.ch
August 26, 2025 at 7:10 AM
🧪 The University of Basel is setting up a new endowed professorship in #ClimateBiophysics at the @biozentrum.unibas.ch, funded by the Georg H. Endress Foundation. This new professorship strengthens climate research @unibas.ch. www.biozentrum.unibas.ch/news/detail/...
Reposted by Philippe Van der Stappen
The Luminal Ring Protein C2CD3 Acts as a Radial In-to-Out Organizer of the Distal Centriole and Appendages pubmed.ncbi.nlm.nih.gov/40667239/ #cryoem
July 17, 2025 at 10:48 AM
The Luminal Ring Protein C2CD3 Acts as a Radial In-to-Out Organizer of the Distal Centriole and Appendages pubmed.ncbi.nlm.nih.gov/40667239/ #cryoem
Reposted by Philippe Van der Stappen
Happy to say that my Current Opinion in Structural Biology article came out today. I hope it helps to guide to you in using cryo-ET to make new biological discoveries!
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
A practical look at cryo-electron tomography image processing: Key considerations for new biological discoveries
Cryo-electron tomography (cryo-ET) enables 3D visualization of complex biological environments without the need for purification, thereby preserving t…
www.sciencedirect.com
July 8, 2025 at 9:44 PM
Happy to say that my Current Opinion in Structural Biology article came out today. I hope it helps to guide to you in using cryo-ET to make new biological discoveries!
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Reposted by Philippe Van der Stappen
🚨 New preprint!
Using U-ExM + in situ cryo-ET, we show how C2CD3 builds an in-to-out radial architecture connecting the distal centriole lumen to its appendages. Great collab with @cellarchlab.com @chgenoud.bsky.social @stearnslab.bsky.social 🙌. #TeamTomo #UExM
www.biorxiv.org/content/10.1...
Using U-ExM + in situ cryo-ET, we show how C2CD3 builds an in-to-out radial architecture connecting the distal centriole lumen to its appendages. Great collab with @cellarchlab.com @chgenoud.bsky.social @stearnslab.bsky.social 🙌. #TeamTomo #UExM
www.biorxiv.org/content/10.1...
June 19, 2025 at 8:58 AM
🚨 New preprint!
Using U-ExM + in situ cryo-ET, we show how C2CD3 builds an in-to-out radial architecture connecting the distal centriole lumen to its appendages. Great collab with @cellarchlab.com @chgenoud.bsky.social @stearnslab.bsky.social 🙌. #TeamTomo #UExM
www.biorxiv.org/content/10.1...
Using U-ExM + in situ cryo-ET, we show how C2CD3 builds an in-to-out radial architecture connecting the distal centriole lumen to its appendages. Great collab with @cellarchlab.com @chgenoud.bsky.social @stearnslab.bsky.social 🙌. #TeamTomo #UExM
www.biorxiv.org/content/10.1...
Reposted by Philippe Van der Stappen
Every machine in a Hospital that diagnoses your body without cutting you open is based on a principle of Physics, discovered by a Physicist who had no interest in Medicine.
If you think the world doesn’t need Basic Science, or that somehow Science has failed you, think again.
If you think the world doesn’t need Basic Science, or that somehow Science has failed you, think again.
June 17, 2025 at 11:22 AM
Every machine in a Hospital that diagnoses your body without cutting you open is based on a principle of Physics, discovered by a Physicist who had no interest in Medicine.
If you think the world doesn’t need Basic Science, or that somehow Science has failed you, think again.
If you think the world doesn’t need Basic Science, or that somehow Science has failed you, think again.
Reposted by Philippe Van der Stappen
Almost all Nobel Prizes are awarded for work that is exploratory, or absolutely basic science with no obvious commercial or medical benefit.
You cannot predict where advancements come from, so you have to invest in science and scientists.
Targeted (corporate) science investment will never do this.
You cannot predict where advancements come from, so you have to invest in science and scientists.
Targeted (corporate) science investment will never do this.
Reminder: Nobel-prize winning PCR (1983), used in basically all genetic tech today, was only possible because of extremophile bacterium discovered in 1964 in Yellowstone funded by a small ~$80k NSF grant with no obvious application at the time. #science 🧪
www.richmondscientific.com/how-a-discov...
www.richmondscientific.com/how-a-discov...
How a discovery in Yellowstone National Park led to the development of PCR - Richmond Scientific
A discovery in Yellowstone National Park led to the development of PCR, the gold-standard COVID-19 tests used to fight the global pandemic.
www.richmondscientific.com
June 8, 2025 at 10:26 PM
Almost all Nobel Prizes are awarded for work that is exploratory, or absolutely basic science with no obvious commercial or medical benefit.
You cannot predict where advancements come from, so you have to invest in science and scientists.
Targeted (corporate) science investment will never do this.
You cannot predict where advancements come from, so you have to invest in science and scientists.
Targeted (corporate) science investment will never do this.
Reposted by Philippe Van der Stappen
"I invite any Trump administration official who thinks our academic standards have declined to sit for an exam in my class. If you can explain the quantum principles underlying the structure of the Periodic Table (like my 18-year-old freshmen can), then you can lecture me on academic standards".
I wrote about the government's attacks on Harvard. Hope this reaches a few persuadable minds.
prosyn.org/PhWi74r?h=Ky...
prosyn.org/PhWi74r?h=Ky...
Defunding Harvard Hurts America | by Adam Ezra Cohen - Project Syndicate
Adam Ezra Cohen explains the real-world consequences of canceling federal research grants in the name of fighting antisemitism.
prosyn.org
June 7, 2025 at 2:58 PM
"I invite any Trump administration official who thinks our academic standards have declined to sit for an exam in my class. If you can explain the quantum principles underlying the structure of the Periodic Table (like my 18-year-old freshmen can), then you can lecture me on academic standards".
Reposted by Philippe Van der Stappen
We’re building a collaborative space for early-career researchers working at the intersection of dinoflagellate taxonomy& molecular biology.
🔗 Learn more: sites.google.com/view/dinosph... 💬 Got questions or input? Please reach out and let us know.
Hope to see you there!
🔗 Learn more: sites.google.com/view/dinosph... 💬 Got questions or input? Please reach out and let us know.
Hope to see you there!
DinoSphere
Welcome
sites.google.com
June 4, 2025 at 4:35 AM
We’re building a collaborative space for early-career researchers working at the intersection of dinoflagellate taxonomy& molecular biology.
🔗 Learn more: sites.google.com/view/dinosph... 💬 Got questions or input? Please reach out and let us know.
Hope to see you there!
🔗 Learn more: sites.google.com/view/dinosph... 💬 Got questions or input? Please reach out and let us know.
Hope to see you there!
Reposted by Philippe Van der Stappen
We’re kicking off the DinoSphere Online Seminar Series! Join us for our first session with Karel Mockaer (Heidelberg) & Yong Heng Phua (OIST)
📅 1 July 9AM CEST
🔗 tinyurl.com/4mjaverj
Spread the word!
@protistwtmostest.bsky.social @ehehenberger.bsky.social @chandnibhickta.bsky.social&Norico Yamada
📅 1 July 9AM CEST
🔗 tinyurl.com/4mjaverj
Spread the word!
@protistwtmostest.bsky.social @ehehenberger.bsky.social @chandnibhickta.bsky.social&Norico Yamada
June 4, 2025 at 4:34 AM
We’re kicking off the DinoSphere Online Seminar Series! Join us for our first session with Karel Mockaer (Heidelberg) & Yong Heng Phua (OIST)
📅 1 July 9AM CEST
🔗 tinyurl.com/4mjaverj
Spread the word!
@protistwtmostest.bsky.social @ehehenberger.bsky.social @chandnibhickta.bsky.social&Norico Yamada
📅 1 July 9AM CEST
🔗 tinyurl.com/4mjaverj
Spread the word!
@protistwtmostest.bsky.social @ehehenberger.bsky.social @chandnibhickta.bsky.social&Norico Yamada
Reposted by Philippe Van der Stappen
Shameless self-promotion continues...🙃 You might find this #fern book in your local bookstores! mailchi.mp/btiscience/f...
May 30, 2025 at 5:03 PM
Shameless self-promotion continues...🙃 You might find this #fern book in your local bookstores! mailchi.mp/btiscience/f...
Reposted by Philippe Van der Stappen
You want to start tomography? Solve structures inside cells? Reach Nyquist 😳 ? @phaips.vd.st and I have a website for you! tomoguide.github.io
You'll find a tutorial on how to reconstruct tomograms, pick particles and do subtomogram averaging, using different software!
Hope it will be useful !
You'll find a tutorial on how to reconstruct tomograms, pick particles and do subtomogram averaging, using different software!
Hope it will be useful !
May 6, 2025 at 4:42 PM
You want to start tomography? Solve structures inside cells? Reach Nyquist 😳 ? @phaips.vd.st and I have a website for you! tomoguide.github.io
You'll find a tutorial on how to reconstruct tomograms, pick particles and do subtomogram averaging, using different software!
Hope it will be useful !
You'll find a tutorial on how to reconstruct tomograms, pick particles and do subtomogram averaging, using different software!
Hope it will be useful !
Hey #TeamTomo,
Ever been in need of a tutorial about the fundamentals of cryo-electron tomography? From preprocessing raw frames to high-res subtomogram averaging?
That's why @florentwaltz.bsky.social and I made this website!
tomoguide.github.io
Follow the thread 1 /🧵
#CryoET #CryoEM 🔬🧪
Ever been in need of a tutorial about the fundamentals of cryo-electron tomography? From preprocessing raw frames to high-res subtomogram averaging?
That's why @florentwaltz.bsky.social and I made this website!
tomoguide.github.io
Follow the thread 1 /🧵
#CryoET #CryoEM 🔬🧪
Welcome to TomoGuide
A step-by-step Cryo-ET guide
tomoguide.github.io
May 6, 2025 at 4:27 PM
Hey #TeamTomo,
Ever been in need of a tutorial about the fundamentals of cryo-electron tomography? From preprocessing raw frames to high-res subtomogram averaging?
That's why @florentwaltz.bsky.social and I made this website!
tomoguide.github.io
Follow the thread 1 /🧵
#CryoET #CryoEM 🔬🧪
Ever been in need of a tutorial about the fundamentals of cryo-electron tomography? From preprocessing raw frames to high-res subtomogram averaging?
That's why @florentwaltz.bsky.social and I made this website!
tomoguide.github.io
Follow the thread 1 /🧵
#CryoET #CryoEM 🔬🧪
Reposted by Philippe Van der Stappen
To all #ChlamyDataset enthusiasts, here is a script that lets you directly import the pre-processed results from EMPIAR-11830 into #RELION v5 for subtomogram averaging:
github.com/Chromatin-St...
#Chlamydomonas #TeamTomo #CryoET #OpenSoftwareAcceleratesScience
github.com/Chromatin-St...
#Chlamydomonas #TeamTomo #CryoET #OpenSoftwareAcceleratesScience
ChlamyAnnotations/chlamydataset2relion5 at master · Chromatin-Structure-Rhythms-Lab/ChlamyAnnotations
Particle annotations for the large-scale cryo-ET dataset of Chlamydomonas reinhardtii - Chromatin-Structure-Rhythms-Lab/ChlamyAnnotations
github.com
April 28, 2025 at 1:16 PM
To all #ChlamyDataset enthusiasts, here is a script that lets you directly import the pre-processed results from EMPIAR-11830 into #RELION v5 for subtomogram averaging:
github.com/Chromatin-St...
#Chlamydomonas #TeamTomo #CryoET #OpenSoftwareAcceleratesScience
github.com/Chromatin-St...
#Chlamydomonas #TeamTomo #CryoET #OpenSoftwareAcceleratesScience
Reposted by Philippe Van der Stappen
🦠🧠 MemBrain update! 🧠🦠
We’ve updated our preprint! It now covers the full MemBrain v2 pipeline for end-to-end membrane analysis in #CryoET: segmentation, particle picking, and spatial statistics.
🔗 Preprint: doi.org/10.1101/2024...
🔗 Code: github.com/CellArchLab/...
🧵(1/6) #TeamTomo
We’ve updated our preprint! It now covers the full MemBrain v2 pipeline for end-to-end membrane analysis in #CryoET: segmentation, particle picking, and spatial statistics.
🔗 Preprint: doi.org/10.1101/2024...
🔗 Code: github.com/CellArchLab/...
🧵(1/6) #TeamTomo
April 25, 2025 at 7:28 AM
🦠🧠 MemBrain update! 🧠🦠
We’ve updated our preprint! It now covers the full MemBrain v2 pipeline for end-to-end membrane analysis in #CryoET: segmentation, particle picking, and spatial statistics.
🔗 Preprint: doi.org/10.1101/2024...
🔗 Code: github.com/CellArchLab/...
🧵(1/6) #TeamTomo
We’ve updated our preprint! It now covers the full MemBrain v2 pipeline for end-to-end membrane analysis in #CryoET: segmentation, particle picking, and spatial statistics.
🔗 Preprint: doi.org/10.1101/2024...
🔗 Code: github.com/CellArchLab/...
🧵(1/6) #TeamTomo
Reposted by Philippe Van der Stappen
Apply now for our international Master of Science in Physics of Life @biozentrum.unibas.ch @unibasel.ch! Scholarships available.
More information: www.biozentrum.unibas.ch/education/de...
#Master #Students #Research #Physics #Mathematics #ComputerScience #Engineering #Basel #Switzerland
More information: www.biozentrum.unibas.ch/education/de...
#Master #Students #Research #Physics #Mathematics #ComputerScience #Engineering #Basel #Switzerland
March 20, 2025 at 8:10 AM
Apply now for our international Master of Science in Physics of Life @biozentrum.unibas.ch @unibasel.ch! Scholarships available.
More information: www.biozentrum.unibas.ch/education/de...
#Master #Students #Research #Physics #Mathematics #ComputerScience #Engineering #Basel #Switzerland
More information: www.biozentrum.unibas.ch/education/de...
#Master #Students #Research #Physics #Mathematics #ComputerScience #Engineering #Basel #Switzerland
Reposted by Philippe Van der Stappen
I'm super happy that our story is now published!
📖 www.science.org/doi/10.1126/...
But what changed compared to the original preprint?
Also, I feel i should post Movie 1 🎥, that inspired the cover. Back when I did the original bluesky thread, movies were not available.
📖 www.science.org/doi/10.1126/...
But what changed compared to the original preprint?
Also, I feel i should post Movie 1 🎥, that inspired the cover. Back when I did the original bluesky thread, movies were not available.
March 21, 2025 at 2:09 PM
I'm super happy that our story is now published!
📖 www.science.org/doi/10.1126/...
But what changed compared to the original preprint?
Also, I feel i should post Movie 1 🎥, that inspired the cover. Back when I did the original bluesky thread, movies were not available.
📖 www.science.org/doi/10.1126/...
But what changed compared to the original preprint?
Also, I feel i should post Movie 1 🎥, that inspired the cover. Back when I did the original bluesky thread, movies were not available.