Rahel Woldeyes
@rahelwoldeyes.bsky.social
Pinned
Rahel Woldeyes
@rahelwoldeyes.bsky.social
· Oct 27
Very excited to share our paper. www.biorxiv.org/content/10.1...
We combine cutting-edge developments in cryo-electron tomography with hiPSC-cardiomyocytes to visualize cardiac proteins in their cellular context in health and disease. #cryoem #teamtomo #cryoet 🧵
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We combine cutting-edge developments in cryo-electron tomography with hiPSC-cardiomyocytes to visualize cardiac proteins in their cellular context in health and disease. #cryoem #teamtomo #cryoet 🧵
1/4
Reposted by Rahel Woldeyes
We developed Adaptive Polishing for the consistent preparation of ~150 nm thin FIB-lamellae. This was done by using imaging feedback to adjust parameters for each lamella, or Adaptive Milling, rather than applying a fixed recipe.
Preprint: doi.org/10.64898/202...
Preprint: doi.org/10.64898/202...
September 23, 2026 at 12:47 PM
We developed Adaptive Polishing for the consistent preparation of ~150 nm thin FIB-lamellae. This was done by using imaging feedback to adjust parameters for each lamella, or Adaptive Milling, rather than applying a fixed recipe.
Preprint: doi.org/10.64898/202...
Preprint: doi.org/10.64898/202...
Reposted by Rahel Woldeyes
EMBL and University of Washington researchers have developed NovoTags – AI-designed protein tags – that in future could help researchers combine fluorescence microscopy and cryo-ET, helping identify individual proteins inside cells. @steffenklein.bsky.social
More info 👉 www.embl.org/news/science...
More info 👉 www.embl.org/news/science...
July 20, 2026 at 1:42 PM
EMBL and University of Washington researchers have developed NovoTags – AI-designed protein tags – that in future could help researchers combine fluorescence microscopy and cryo-ET, helping identify individual proteins inside cells. @steffenklein.bsky.social
More info 👉 www.embl.org/news/science...
More info 👉 www.embl.org/news/science...
Reposted by Rahel Woldeyes
The labs of KC Huang and Justin Sonnenburg at Stanford are working on an exciting and impactful project related to infant probiotics and are hiring a Life Science Research Professional to be part of that team.
Take a look at the posting if you're interested.
Please share/apply
Take a look at the posting if you're interested.
Please share/apply
Life Science Research Professional 2
Applying a comprehensive understanding for the theories and methods of a life science discipline, perform work directly involved in research projects, interpreting results and participation in experim...
careersearch.stanford.edu
July 17, 2026 at 12:26 AM
The labs of KC Huang and Justin Sonnenburg at Stanford are working on an exciting and impactful project related to infant probiotics and are hiring a Life Science Research Professional to be part of that team.
Take a look at the posting if you're interested.
Please share/apply
Take a look at the posting if you're interested.
Please share/apply
Reposted by Rahel Woldeyes
A beautiful journey through the nuclear pore complex with #cryoET - samples prepared via the Arctis Cryo-Plasma-FIB, data collected with the Glacios Cryo-TEM and segmented in Amira Software.
#TeamTomo - See what’s possible with 200 kV cryo-ET: ter.li/n2a8i5po
#TeamTomo - See what’s possible with 200 kV cryo-ET: ter.li/n2a8i5po
July 14, 2026 at 6:37 PM
A beautiful journey through the nuclear pore complex with #cryoET - samples prepared via the Arctis Cryo-Plasma-FIB, data collected with the Glacios Cryo-TEM and segmented in Amira Software.
#TeamTomo - See what’s possible with 200 kV cryo-ET: ter.li/n2a8i5po
#TeamTomo - See what’s possible with 200 kV cryo-ET: ter.li/n2a8i5po
Reposted by Rahel Woldeyes
Microscopy nerd alert: two scopes in California can now do phase contrast cryoEM - potentially fixing the tech's very low signal/noise ratio.
The phase filter they used is a laser. Which is also the brightest thing in the solar system (outside of the inside of the sun).
cen.acs.org/analytical-c...
The phase filter they used is a laser. Which is also the brightest thing in the solar system (outside of the inside of the sun).
cen.acs.org/analytical-c...
15 years, flawless mirrors, and the brightest laser in the world: How physicists brought phase contrast to cryo-EM
Phase contrast enables structures of smaller proteins, could drive in-cell proteomics
cen.acs.org
June 11, 2026 at 6:38 PM
Microscopy nerd alert: two scopes in California can now do phase contrast cryoEM - potentially fixing the tech's very low signal/noise ratio.
The phase filter they used is a laser. Which is also the brightest thing in the solar system (outside of the inside of the sun).
cen.acs.org/analytical-c...
The phase filter they used is a laser. Which is also the brightest thing in the solar system (outside of the inside of the sun).
cen.acs.org/analytical-c...
Reposted by Rahel Woldeyes
In a series of 3 papers and preprints, we’re thrilled to share with you the working laser phase plate. In collaboration with research led by Holger Müller at UC Berkeley, this is a huge innovation in imaging to make small and faint objects inside cells visible. bit.ly/4vK9LVn
June 11, 2026 at 6:02 PM
In a series of 3 papers and preprints, we’re thrilled to share with you the working laser phase plate. In collaboration with research led by Holger Müller at UC Berkeley, this is a huge innovation in imaging to make small and faint objects inside cells visible. bit.ly/4vK9LVn
Reposted by Rahel Woldeyes
Better vitrification = better cryo-ET.
We've opened an RFA for two-year grants to advance vitrification techniques for biological samples—welcoming applications from researchers in heat transfer, cryogenics, and materials science.
Apply here: bit.ly/4uip6eJ
We've opened an RFA for two-year grants to advance vitrification techniques for biological samples—welcoming applications from researchers in heat transfer, cryogenics, and materials science.
Apply here: bit.ly/4uip6eJ
June 4, 2026 at 6:24 PM
Better vitrification = better cryo-ET.
We've opened an RFA for two-year grants to advance vitrification techniques for biological samples—welcoming applications from researchers in heat transfer, cryogenics, and materials science.
Apply here: bit.ly/4uip6eJ
We've opened an RFA for two-year grants to advance vitrification techniques for biological samples—welcoming applications from researchers in heat transfer, cryogenics, and materials science.
Apply here: bit.ly/4uip6eJ
Reposted by Rahel Woldeyes
Excited to share our work uncovering SNOR, a ribosome-associated factor that promotes translation restart after dormancy published in Nature!! This was, as usual, a wonderful collaborative effort between our group and the Mattei Lab @simonemattei.bsky.social @embl.org www.nature.com/articles/s41...
May 13, 2026 at 3:34 PM
Excited to share our work uncovering SNOR, a ribosome-associated factor that promotes translation restart after dormancy published in Nature!! This was, as usual, a wonderful collaborative effort between our group and the Mattei Lab @simonemattei.bsky.social @embl.org www.nature.com/articles/s41...
Reposted by Rahel Woldeyes
First PROTAC gains FDA approval, bolstering targeted protein degradation and induced proximity ambitions www.nature.com/articles/d41...
First PROTAC gains FDA approval, bolstering targeted protein degradation and induced proximity ambitions
Discover the world’s best science and medicine | Nature.com
www.nature.com
May 9, 2026 at 1:31 AM
First PROTAC gains FDA approval, bolstering targeted protein degradation and induced proximity ambitions www.nature.com/articles/d41...
Reposted by Rahel Woldeyes
Today we're launching the Open Source for Science Fund, a new multi-donor philanthropic fund by Renaissance Philanthropy, seeded by @biohub.org and @wellcometrust.bsky.social, with support from @kavlifoundation.org and @researchsoftware.bsky.social
🧵 os4science.org/news/open-so...
🧵 os4science.org/news/open-so...
Open Source for Science Fund Launches to Power AI-Driven Discovery
A new multi-donor fund by Renaissance Philanthropy seeded by Biohub and Wellcome opens its first call for proposals.
os4science.org
May 4, 2026 at 4:41 PM
Today we're launching the Open Source for Science Fund, a new multi-donor philanthropic fund by Renaissance Philanthropy, seeded by @biohub.org and @wellcometrust.bsky.social, with support from @kavlifoundation.org and @researchsoftware.bsky.social
🧵 os4science.org/news/open-so...
🧵 os4science.org/news/open-so...
Reposted by Rahel Woldeyes
We're super excited to share MissAlignment: a new ML-based approach to reference-free tilt series alignment, spearheaded by @martenchaillet.bsky.social. We think it's going to make your cryo-ET life a lot better.
Preprint: www.biorxiv.org/content/10.6...
Code: github.com/warpem/miss-...
🧶 Thread:
Preprint: www.biorxiv.org/content/10.6...
Code: github.com/warpem/miss-...
🧶 Thread:
May 3, 2026 at 6:11 AM
We're super excited to share MissAlignment: a new ML-based approach to reference-free tilt series alignment, spearheaded by @martenchaillet.bsky.social. We think it's going to make your cryo-ET life a lot better.
Preprint: www.biorxiv.org/content/10.6...
Code: github.com/warpem/miss-...
🧶 Thread:
Preprint: www.biorxiv.org/content/10.6...
Code: github.com/warpem/miss-...
🧶 Thread:
Reposted by Rahel Woldeyes
Today we're announcing the Virtual Biology Initiative—a major new commitment to build the data foundation biology needs to power the next generation of AI models. Next-gen imaging. Molecular engineering tools. Open data infrastructure for the entire scientific community.
Read more: bit.ly/3ONTkHO
Read more: bit.ly/3ONTkHO
Biohub launches the Virtual Biology Initiative
A $500M commitment to galvanize a global, open-data effort to build predictive models of the human cell.
bit.ly
April 29, 2026 at 3:05 PM
Today we're announcing the Virtual Biology Initiative—a major new commitment to build the data foundation biology needs to power the next generation of AI models. Next-gen imaging. Molecular engineering tools. Open data infrastructure for the entire scientific community.
Read more: bit.ly/3ONTkHO
Read more: bit.ly/3ONTkHO
Reposted by Rahel Woldeyes
Preprint 🧵!
I’m really excited to introduce BIGSMALL, an interleaved multi-magnification cryo-ET scheme bridging molecular and cellular scales in a single acquisition!
BIGSMALL = 𝐁road 𝐈nformation 𝐆athering 𝐒trategy by 𝐌ultiscale 𝐀cquisition of lame𝐋𝐋a
www.biorxiv.org/content/10.6... (1/6)
I’m really excited to introduce BIGSMALL, an interleaved multi-magnification cryo-ET scheme bridging molecular and cellular scales in a single acquisition!
BIGSMALL = 𝐁road 𝐈nformation 𝐆athering 𝐒trategy by 𝐌ultiscale 𝐀cquisition of lame𝐋𝐋a
www.biorxiv.org/content/10.6... (1/6)
April 25, 2026 at 7:25 AM
Preprint 🧵!
I’m really excited to introduce BIGSMALL, an interleaved multi-magnification cryo-ET scheme bridging molecular and cellular scales in a single acquisition!
BIGSMALL = 𝐁road 𝐈nformation 𝐆athering 𝐒trategy by 𝐌ultiscale 𝐀cquisition of lame𝐋𝐋a
www.biorxiv.org/content/10.6... (1/6)
I’m really excited to introduce BIGSMALL, an interleaved multi-magnification cryo-ET scheme bridging molecular and cellular scales in a single acquisition!
BIGSMALL = 𝐁road 𝐈nformation 𝐆athering 𝐒trategy by 𝐌ultiscale 𝐀cquisition of lame𝐋𝐋a
www.biorxiv.org/content/10.6... (1/6)
Reposted by Rahel Woldeyes
Excited to share our paper about copick, a dataset API and toolkit for collaborative annotation and analysis of #cryoET data! Whether you're picking particles or curating segmentations, copick reduces friction and brings #OME-Zarr to cryoET without breaking pipelines.
🧵👇
doi.org/10.1002/pro.70578
🧵👇
doi.org/10.1002/pro.70578
April 20, 2026 at 5:32 PM
Excited to share our paper about copick, a dataset API and toolkit for collaborative annotation and analysis of #cryoET data! Whether you're picking particles or curating segmentations, copick reduces friction and brings #OME-Zarr to cryoET without breaking pipelines.
🧵👇
doi.org/10.1002/pro.70578
🧵👇
doi.org/10.1002/pro.70578
Reposted by Rahel Woldeyes
Check out our new release on BioRxiv
co-lead by @pm-mueller.bsky.social
👉 rb.gy/lnrizk
special🙏 to
Severine Kunz #MDC
@leventallab.bsky.social
@andimicroscopy.bsky.social
@ewerslab.bsky.social and Kedar Narayan @NCI CCR VolumeEM
Are the days of discovering new cellular structures over?? /1
co-lead by @pm-mueller.bsky.social
👉 rb.gy/lnrizk
special🙏 to
Severine Kunz #MDC
@leventallab.bsky.social
@andimicroscopy.bsky.social
@ewerslab.bsky.social and Kedar Narayan @NCI CCR VolumeEM
Are the days of discovering new cellular structures over?? /1
April 15, 2026 at 4:52 PM
Check out our new release on BioRxiv
co-lead by @pm-mueller.bsky.social
👉 rb.gy/lnrizk
special🙏 to
Severine Kunz #MDC
@leventallab.bsky.social
@andimicroscopy.bsky.social
@ewerslab.bsky.social and Kedar Narayan @NCI CCR VolumeEM
Are the days of discovering new cellular structures over?? /1
co-lead by @pm-mueller.bsky.social
👉 rb.gy/lnrizk
special🙏 to
Severine Kunz #MDC
@leventallab.bsky.social
@andimicroscopy.bsky.social
@ewerslab.bsky.social and Kedar Narayan @NCI CCR VolumeEM
Are the days of discovering new cellular structures over?? /1
Reposted by Rahel Woldeyes
Across scales from cells🦠 to atoms⚛️ – We reveal how anaerobic #bacteria break down very stable aromatic compounds found e.g. in oil spills 🛢️ #Bioremediation #TeamTomo 🧪 🧶🧬 🔬
Awesome collab with Lena, Matthias, @schullerjm.bsky.social @rnfr2d2.bsky.social @tomaspascoa.bsky.social @tamb-o.bsky.social
Awesome collab with Lena, Matthias, @schullerjm.bsky.social @rnfr2d2.bsky.social @tomaspascoa.bsky.social @tamb-o.bsky.social
April 14, 2026 at 3:31 PM
Across scales from cells🦠 to atoms⚛️ – We reveal how anaerobic #bacteria break down very stable aromatic compounds found e.g. in oil spills 🛢️ #Bioremediation #TeamTomo 🧪 🧶🧬 🔬
Awesome collab with Lena, Matthias, @schullerjm.bsky.social @rnfr2d2.bsky.social @tomaspascoa.bsky.social @tamb-o.bsky.social
Awesome collab with Lena, Matthias, @schullerjm.bsky.social @rnfr2d2.bsky.social @tomaspascoa.bsky.social @tamb-o.bsky.social
Reposted by Rahel Woldeyes
💪 NEW VIDEO:
Flying over the A-band of an atomic-scale model of a vertebrate muscle sarcomere. Let's explore the molecular mechanics that make your muscles work.
Rendered using @bradyajohnston.bsky.social 's molecular nodes
Model based on the incredible work of the @raunser-lab.bsky.social lab
Flying over the A-band of an atomic-scale model of a vertebrate muscle sarcomere. Let's explore the molecular mechanics that make your muscles work.
Rendered using @bradyajohnston.bsky.social 's molecular nodes
Model based on the incredible work of the @raunser-lab.bsky.social lab
January 31, 2026 at 3:00 PM
💪 NEW VIDEO:
Flying over the A-band of an atomic-scale model of a vertebrate muscle sarcomere. Let's explore the molecular mechanics that make your muscles work.
Rendered using @bradyajohnston.bsky.social 's molecular nodes
Model based on the incredible work of the @raunser-lab.bsky.social lab
Flying over the A-band of an atomic-scale model of a vertebrate muscle sarcomere. Let's explore the molecular mechanics that make your muscles work.
Rendered using @bradyajohnston.bsky.social 's molecular nodes
Model based on the incredible work of the @raunser-lab.bsky.social lab
Reposted by Rahel Woldeyes
www.nature.com/articles/s41... 🧪. DeepMind AlphaGenome, trained on 1 Mb of DNA sequence from human and mouse and predicts thousands of functional genomic tracks including gene expression, transcription initiation, chromatin accessibility, histone modifications, transcription factor binding etc
Advancing regulatory variant effect prediction with AlphaGenome - Nature
AlphaGenome, a deep learning model that inputs 1-Mb DNA sequence to predict functional genomic tracks at single-base resolution across diverse modalities, outperforms existing models in variant effect...
www.nature.com
January 29, 2026 at 11:31 AM
www.nature.com/articles/s41... 🧪. DeepMind AlphaGenome, trained on 1 Mb of DNA sequence from human and mouse and predicts thousands of functional genomic tracks including gene expression, transcription initiation, chromatin accessibility, histone modifications, transcription factor binding etc
New on the CryoET Data Portal: ~27,000 tomograms of affinity-captured lysosomes from HEK293T cells across 4 physiological states. Includes raw data, AreTomo3 reconstructions & Membrain-Seg annotations. Openly available for reuse!
cryoetdataportal.czscience.com/depositions/...
cryoetdataportal.czscience.com/depositions/...
January 27, 2026 at 11:26 PM
Reposted by Rahel Woldeyes
New on the CryoET Data Portal: ~27,000 tomograms of affinity-captured lysosomes from HEK293T cells across 4 physiological states. Includes raw data, AreTomo3 reconstructions & Membrain-Seg annotations. Openly available for reuse!
cryoetdataportal.czscience.com/depositions/...
cryoetdataportal.czscience.com/depositions/...
January 27, 2026 at 7:59 PM
New on the CryoET Data Portal: ~27,000 tomograms of affinity-captured lysosomes from HEK293T cells across 4 physiological states. Includes raw data, AreTomo3 reconstructions & Membrain-Seg annotations. Openly available for reuse!
cryoetdataportal.czscience.com/depositions/...
cryoetdataportal.czscience.com/depositions/...
Reposted by Rahel Woldeyes
Huge congrats to @manuelthery.bsky.social and all the Cytomorpho lab. The "Living Architectures" performance at @museeorsay.bsky.social was breathtakingly beautiful
January 25, 2026 at 9:22 AM
Huge congrats to @manuelthery.bsky.social and all the Cytomorpho lab. The "Living Architectures" performance at @museeorsay.bsky.social was breathtakingly beautiful
Reposted by Rahel Woldeyes
IsoNet2 determines cellular structures at submolecular resolution without averaging [new]
3D cryo-ET recon: self-sup. DL refines struct., revealing details in situ.
3D cryo-ET recon: self-sup. DL refines struct., revealing details in situ.
December 11, 2025 at 11:43 AM
IsoNet2 determines cellular structures at submolecular resolution without averaging [new]
3D cryo-ET recon: self-sup. DL refines struct., revealing details in situ.
3D cryo-ET recon: self-sup. DL refines struct., revealing details in situ.
Reposted by Rahel Woldeyes
#LivingArchitectures
We put cells and cytoskeleton filaments on the architecture of the musée d'Orsay.
www.musee-orsay.fr/fr/agenda/ev...
Scientists of the #CytoMorphoLab adapted their protocols to illustrate the questions that keep them awake at night.
-> Two shows on the 24th and 25th of January.
We put cells and cytoskeleton filaments on the architecture of the musée d'Orsay.
www.musee-orsay.fr/fr/agenda/ev...
Scientists of the #CytoMorphoLab adapted their protocols to illustrate the questions that keep them awake at night.
-> Two shows on the 24th and 25th of January.
December 5, 2025 at 4:11 PM
#LivingArchitectures
We put cells and cytoskeleton filaments on the architecture of the musée d'Orsay.
www.musee-orsay.fr/fr/agenda/ev...
Scientists of the #CytoMorphoLab adapted their protocols to illustrate the questions that keep them awake at night.
-> Two shows on the 24th and 25th of January.
We put cells and cytoskeleton filaments on the architecture of the musée d'Orsay.
www.musee-orsay.fr/fr/agenda/ev...
Scientists of the #CytoMorphoLab adapted their protocols to illustrate the questions that keep them awake at night.
-> Two shows on the 24th and 25th of January.
Reposted by Rahel Woldeyes
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...