Ricardo D. Righetto
@lifeonthewedge.bsky.social
Staff scientist @biozentrum.unibas.ch using algorithms to look at tiny stuff inside cells, or #cryoET if you prefer. Here I talk mostly about my research. Views my own. 🇧🇷 in 🇨🇭
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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
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🍧
Reposted by Ricardo D. Righetto
Note: this bug only affects v0.3, results from v0.2 should be fine 😉
December 3, 2025 at 12:43 PM
Note: this bug only affects v0.3, results from v0.2 should be fine 😉
We just released version v0.3.1 of 🍦Icecream!
Importantly, this fixes a bug in missing wedge correction. Please update, and let us know how it works for you!
#CryoET #TeamTomo
github.com/swing-resear...
Importantly, this fixes a bug in missing wedge correction. Please update, and let us know how it works for you!
#CryoET #TeamTomo
github.com/swing-resear...
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
December 3, 2025 at 9:22 AM
We just released version v0.3.1 of 🍦Icecream!
Importantly, this fixes a bug in missing wedge correction. Please update, and let us know how it works for you!
#CryoET #TeamTomo
github.com/swing-resear...
Importantly, this fixes a bug in missing wedge correction. Please update, and let us know how it works for you!
#CryoET #TeamTomo
github.com/swing-resear...
not a coincidence 😉🦑
December 2, 2025 at 10:21 AM
not a coincidence 😉🦑
Reposted by Ricardo D. Righetto
Did you know we’re hosting the EMBO Practical Course on Cryo-FIB & Cryo-ET in April 2026? ❄️ We invite early career researchers and facility scientists to join us in Frankfurt and meet the leading experts in cryo-FIB/SEM and cryo-ET!
🔗 Apply by Dec 8: meetings.embo.org/event/26-in-...
🔗 Apply by Dec 8: meetings.embo.org/event/26-in-...
December 2, 2025 at 9:32 AM
Did you know we’re hosting the EMBO Practical Course on Cryo-FIB & Cryo-ET in April 2026? ❄️ We invite early career researchers and facility scientists to join us in Frankfurt and meet the leading experts in cryo-FIB/SEM and cryo-ET!
🔗 Apply by Dec 8: meetings.embo.org/event/26-in-...
🔗 Apply by Dec 8: meetings.embo.org/event/26-in-...
Reposted by Ricardo D. Righetto
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!
Reposted by Ricardo D. Righetto
Are you looking for female speakers in CryoEM for seminars and conferences? Are you a woman in CryoEM and not yet on the ‚woman in CryoEM‘ list? Find your speakers and add/update name and affiliation! docs.google.com/spreadsheets...
November 18, 2025 at 10:18 AM
Are you looking for female speakers in CryoEM for seminars and conferences? Are you a woman in CryoEM and not yet on the ‚woman in CryoEM‘ list? Find your speakers and add/update name and affiliation! docs.google.com/spreadsheets...
Reposted by Ricardo D. Righetto
Hi #teamtomo! Want to use OME-Zarr for your tilt series but can't integrate it with your existing sub-tomogram averaging pipelines?
Try zarr-particle-tools - RELION-style extraction & reconstruction built for OME-Zarr-based workflows!
📦 pip install zarr-particle-tools
🔗 github.com/czimagingins...
Try zarr-particle-tools - RELION-style extraction & reconstruction built for OME-Zarr-based workflows!
📦 pip install zarr-particle-tools
🔗 github.com/czimagingins...
GitHub - czimaginginstitute/zarr-particle-tools: Particle extraction and reconstruction from OME-Zarr tilt series.
Particle extraction and reconstruction from OME-Zarr tilt series. - czimaginginstitute/zarr-particle-tools
github.com
November 17, 2025 at 10:30 PM
Hi #teamtomo! Want to use OME-Zarr for your tilt series but can't integrate it with your existing sub-tomogram averaging pipelines?
Try zarr-particle-tools - RELION-style extraction & reconstruction built for OME-Zarr-based workflows!
📦 pip install zarr-particle-tools
🔗 github.com/czimagingins...
Try zarr-particle-tools - RELION-style extraction & reconstruction built for OME-Zarr-based workflows!
📦 pip install zarr-particle-tools
🔗 github.com/czimagingins...
Reposted by Ricardo D. Righetto
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
Reposted by Ricardo D. Righetto
I am excited to share our new preprint on our structural and biochemical analyses of human methionine synthase (MTR). This was the hard work of Douglas Ferreira who carried out this research as a significant part of his PhD. #CryoEM www.biorxiv.org/content/10.1...
Structural insights into cobalamin loading and reactivation of human methionine synthase
Human methionine synthase (MTR) is an essential enzyme of one carbon metabolism. Consisting of a catalytic N-half and a cobalamin binding C-half, MTR utilises this intricate organometallic cofactor in...
www.biorxiv.org
November 11, 2025 at 12:48 PM
I am excited to share our new preprint on our structural and biochemical analyses of human methionine synthase (MTR). This was the hard work of Douglas Ferreira who carried out this research as a significant part of his PhD. #CryoEM www.biorxiv.org/content/10.1...
Reposted by Ricardo D. Righetto
Last week, the Dodonova lab published a fascinating paper on chromatin structures in Asgard archaea, microbes thought to be the closest relatives of complex life.
Asgard histones can wrap DNA into a “closed” form shared across archaea, and an “open” form similar to eukaryotic cells #sciart #blender
Asgard histones can wrap DNA into a “closed” form shared across archaea, and an “open” form similar to eukaryotic cells #sciart #blender
November 11, 2025 at 10:41 AM
Many Stentors were harmed in this study
(and it's great)
(and it's great)
Wound healing is a hallmark feature of all life, including single cells. In a new preprint, Ambika Nadkarni @biochembika.bsky.social investigates a new dimension in cellular wound healing: how cells recover AFTER the wound has been closed
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
November 11, 2025 at 9:36 PM
Many Stentors were harmed in this study
(and it's great)
(and it's great)
Reposted by Ricardo D. Righetto
An Asgard archaeon with internal membrane compartments
Brilliant study led by @fmacleod.bsky.social and Andriko von Kügelgen. Tight collaboration with @buzzbaum.bsky.social and lab. Congrats to all authors!
www.biorxiv.org/content/10.1...
Brilliant study led by @fmacleod.bsky.social and Andriko von Kügelgen. Tight collaboration with @buzzbaum.bsky.social and lab. Congrats to all authors!
www.biorxiv.org/content/10.1...
November 7, 2025 at 10:44 AM
An Asgard archaeon with internal membrane compartments
Brilliant study led by @fmacleod.bsky.social and Andriko von Kügelgen. Tight collaboration with @buzzbaum.bsky.social and lab. Congrats to all authors!
www.biorxiv.org/content/10.1...
Brilliant study led by @fmacleod.bsky.social and Andriko von Kügelgen. Tight collaboration with @buzzbaum.bsky.social and lab. Congrats to all authors!
www.biorxiv.org/content/10.1...
Reposted by Ricardo D. Righetto
Our new preprint is out 🥳🥳🥳
Henipaviruses, like Nipah and Hendra, package their genomes inside helical shells built by thousands of nucleoproteins. These nucleocapsids are essential to protect the viral RNA, but how do they ever let the polymerase in to read the sequence?
👇
Henipaviruses, like Nipah and Hendra, package their genomes inside helical shells built by thousands of nucleoproteins. These nucleocapsids are essential to protect the viral RNA, but how do they ever let the polymerase in to read the sequence?
👇
November 3, 2025 at 12:26 PM
Our new preprint is out 🥳🥳🥳
Henipaviruses, like Nipah and Hendra, package their genomes inside helical shells built by thousands of nucleoproteins. These nucleocapsids are essential to protect the viral RNA, but how do they ever let the polymerase in to read the sequence?
👇
Henipaviruses, like Nipah and Hendra, package their genomes inside helical shells built by thousands of nucleoproteins. These nucleocapsids are essential to protect the viral RNA, but how do they ever let the polymerase in to read the sequence?
👇
This is pretty cool!
Undergrads @biozentrum.unibas.ch are learning RFdiffusion at our Structural Biology Block Course organized by @computingcaitie.bsky.social, Basile Wicky et al. 😉
www.nature.com/articles/s41...
Undergrads @biozentrum.unibas.ch are learning RFdiffusion at our Structural Biology Block Course organized by @computingcaitie.bsky.social, Basile Wicky et al. 😉
www.nature.com/articles/s41...
Atomically accurate de novo design of antibodies with RFdiffusion - Nature
The combination of computational design, laboratory-based screening and biophysical validation enables the de novo generation of variable heavy-chain antibody fragments and antibodies that precis...
www.nature.com
November 6, 2025 at 11:19 AM
This is pretty cool!
Undergrads @biozentrum.unibas.ch are learning RFdiffusion at our Structural Biology Block Course organized by @computingcaitie.bsky.social, Basile Wicky et al. 😉
www.nature.com/articles/s41...
Undergrads @biozentrum.unibas.ch are learning RFdiffusion at our Structural Biology Block Course organized by @computingcaitie.bsky.social, Basile Wicky et al. 😉
www.nature.com/articles/s41...
Reposted by Ricardo D. Righetto
Excited to share our latest @nature.com: How does naloxone (Narcan) stop an opioid overdose? We determined the first GDP-bound μ-opioid receptor–G protein structures and found naloxone traps a novel "latent” state, preventing GDP release and G protein activation.💊🧪 🧵👇 www.nature.com/articles/s41...
November 5, 2025 at 4:23 PM
Excited to share our latest @nature.com: How does naloxone (Narcan) stop an opioid overdose? We determined the first GDP-bound μ-opioid receptor–G protein structures and found naloxone traps a novel "latent” state, preventing GDP release and G protein activation.💊🧪 🧵👇 www.nature.com/articles/s41...
Reposted by Ricardo D. Righetto
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 28, 2025 at 3:07 PM
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...
Reposted by Ricardo D. Righetto
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 4, 2025 at 5:30 PM
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/...
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 😉
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 5, 2025 at 2:41 PM
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! 🙏🏽
Reposted by Ricardo D. Righetto
imigração é um direito. fronteiras são inventadas. bichos migram, os seres humanos sempre mudaram de lugar.
I think this constant push for immigrants to feel & act ‘grateful’ is so insidious. Let’s change the narrative. Migration is a normal part of human behaviour, not a charity case. If you’re doing your best to do your best, you don’t need to do even more to be accepted. It’s your right to be accepted.
November 5, 2025 at 7:20 AM
imigração é um direito. fronteiras são inventadas. bichos migram, os seres humanos sempre mudaram de lugar.
Reposted by Ricardo D. Righetto
Remember when Aaron Swartz downloaded JSTOR archives that he had full legal rights to download and the FBI hounded him literally to death for it? Anyway,
NEW: Common Crawl, the massive archiver of the web, has gotten cozy with AI companies and is providing paywalled articles for training data. They’re also lying to publishers who have asked for material to be removed. “The robots are people too,” CC’s exec director told us when we asked about this.
The Nonprofit Feeding the Entire Internet to AI Companies
Common Crawl claims to provide a public benefit, but it lies to publishers about its activities.
www.theatlantic.com
November 4, 2025 at 2:06 PM
Remember when Aaron Swartz downloaded JSTOR archives that he had full legal rights to download and the FBI hounded him literally to death for it? Anyway,
Reposted by Ricardo D. Righetto
Neutralizing antibodies against Chikungunya virus and structural elucidation of their mechanism of action pubmed.ncbi.nlm.nih.gov/41184282/ #cryoem
November 4, 2025 at 10:15 AM
Neutralizing antibodies against Chikungunya virus and structural elucidation of their mechanism of action pubmed.ncbi.nlm.nih.gov/41184282/ #cryoem
Reposted by Ricardo D. Righetto
CryoWriter: A Robotic Solution for Improved Cryo-EM Grid Preparation https://www.biorxiv.org/content/10.1101/2025.11.01.686008v1
November 3, 2025 at 1:47 AM
CryoWriter: A Robotic Solution for Improved Cryo-EM Grid Preparation https://www.biorxiv.org/content/10.1101/2025.11.01.686008v1
Reposted by Ricardo D. Righetto
November 2, 2025 at 9:24 AM
Reposted by Ricardo D. Righetto
And it’s a double feature, as shown by @gautamdey.bsky.social ial & @floravincent.bsky.social for the sturdy #Diatoms! Also out today in @currentbiology.bsky.social 🌊
www.cell.com/current-biol...
www.cell.com/current-biol...
Diatom ultrastructural diversity across controlled and natural environments
Flori et al. establish high-resolution and generalizable immunofluorescence in cultured
and environmental diatoms, thanks to 4-fold cryo-expansion microscopy. This represents
a step-change for compara...
www.cell.com
October 31, 2025 at 2:42 PM
And it’s a double feature, as shown by @gautamdey.bsky.social ial & @floravincent.bsky.social for the sturdy #Diatoms! Also out today in @currentbiology.bsky.social 🌊
www.cell.com/current-biol...
www.cell.com/current-biol...