December 28, 2025 at 4:37 AM
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 😉
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...
🧬Great lineup of speakers!
@rommieamaro.bsky.social @jessicaandreani.bsky.social @gauravbhardwaj.bsky.social @bonomimax.bsky.social @rocovino.bsky.social @bioinfo.se Sergei Grudinin @magistratolab.bsky.social Christine Orengo @joanampereira.bsky.social Maya Topf, Sameer Velankar, Basile Wicky
@rommieamaro.bsky.social @jessicaandreani.bsky.social @gauravbhardwaj.bsky.social @bonomimax.bsky.social @rocovino.bsky.social @bioinfo.se Sergei Grudinin @magistratolab.bsky.social Christine Orengo @joanampereira.bsky.social Maya Topf, Sameer Velankar, Basile Wicky
May 27, 2025 at 5:51 PM
MissAlignment is here to align all our Bananas🍌 and Birds🦅 into beautiful Pineapples🍍 ...Did that make sense? Either way, read Dimitry's thread🧵 for a vivid visual demonstration. This new software cooks! Look how crispy it made the #ChlamyDataset nucleosome👇. #TeamTomo is hitting escape velocity 🚀 🧪
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 2:35 PM
MissAlignment is here to align all our Bananas🍌 and Birds🦅 into beautiful Pineapples🍍 ...Did that make sense? Either way, read Dimitry's thread🧵 for a vivid visual demonstration. This new software cooks! Look how crispy it made the #ChlamyDataset nucleosome👇. #TeamTomo is hitting escape velocity 🚀 🧪
The #ChlamyDataset has now been used to elucidate the protein extensions of the #chloroplast #ribosome 💚
Long in the making, but happy to present the Chlamydomonas chlororibosome!
Cryo-ET🔬reveals a large new domain on the small subunit, built from multiple extensions in conserved ribosomal proteins.
bioRxiv 📖: shorturl.at/q44tG
This suggests greater chlororibosome diversity than expected!
1/n 🧵
Cryo-ET🔬reveals a large new domain on the small subunit, built from multiple extensions in conserved ribosomal proteins.
bioRxiv 📖: shorturl.at/q44tG
This suggests greater chlororibosome diversity than expected!
1/n 🧵
February 10, 2026 at 2:57 PM
The #ChlamyDataset has now been used to elucidate the protein extensions of the #chloroplast #ribosome 💚
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...
For a starter, #MemBrain-seg from @lorenzlamm.bsky.social would not have been possible without the #ChlamyDataset and lots of other kind contributions from the #CryoET community 🙏🏽
#TeamTomo
#TeamTomo
🦠🧠 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
January 9, 2026 at 7:15 PM
For a starter, #MemBrain-seg from @lorenzlamm.bsky.social would not have been possible without the #ChlamyDataset and lots of other kind contributions from the #CryoET community 🙏🏽
#TeamTomo
#TeamTomo
My colleagues @phaips.vd.st and @florentwaltz.bsky.social have put together this wonderful website with step-by-step tutorials for in situ subtomogram averaging using different software packages 🤩
Check it out, especially if you are a newcomer to the field!
#CryoET #TeamTomo #ChlamyDataset
Check it out, especially if you are a newcomer to the field!
#CryoET #TeamTomo #ChlamyDataset
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 7, 2025 at 6:28 AM
My colleagues @phaips.vd.st and @florentwaltz.bsky.social have put together this wonderful website with step-by-step tutorials for in situ subtomogram averaging using different software packages 🤩
Check it out, especially if you are a newcomer to the field!
#CryoET #TeamTomo #ChlamyDataset
Check it out, especially if you are a newcomer to the field!
#CryoET #TeamTomo #ChlamyDataset
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
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 7:15 PM
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]
🍦IceCream, a denoising and missing wedge estimation tool, has also relied a lot on the #ChlamyDataset for development:
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
January 9, 2026 at 7:15 PM
🍦IceCream, a denoising and missing wedge estimation tool, has also relied a lot on the #ChlamyDataset for development:
The #ChlamyDataset is intended to be a public resource for methods development and scientific discovery, and I'm happy to say it has been adopted very early by the #CryoET community, even before the preprint was out. So below I’ll highlight some of the cool stuff that have been done with it 🤗
January 9, 2026 at 7:15 PM
The #ChlamyDataset is intended to be a public resource for methods development and scientific discovery, and I'm happy to say it has been adopted very early by the #CryoET community, even before the preprint was out. So below I’ll highlight some of the cool stuff that have been done with it 🤗
This is less than 2 years after releasing the dataset and 1 year after the #preprint – and I'm sure more stuff is on the way. Apologies if I have missed some method or application based on the #ChlamyDataset – please let me know, will be happy to include it in the thread!
January 9, 2026 at 7:15 PM
This is less than 2 years after releasing the dataset and 1 year after the #preprint – and I'm sure more stuff is on the way. Apologies if I have missed some method or application based on the #ChlamyDataset – please let me know, will be happy to include it in the thread!
#PickET is a pretty cool semantic segmentation and particle picker tool that was also demonstrated on the #ChlamyDataset:
PickET: An unsupervised method for localizing macromolecules in cryo-electron tomograms
Cryo-electron tomography (cryo-ET) datasets are rich sources of information capable of describing the localizations, structures, and interactions of macromolecules. However, most current methods for l...
www.biorxiv.org
January 9, 2026 at 7:15 PM
#PickET is a pretty cool semantic segmentation and particle picker tool that was also demonstrated on the #ChlamyDataset:
Thanks Japan for using the #ChlamyDataset
Chlamy Hello Kitty at the Japan Pavilion Osaka Expo 2025
August 8, 2025 at 11:20 AM
Thanks Japan for using the #ChlamyDataset