🎉 Our paper “MIFA: Metadata, Incentives, Formats and Accessibility guidelines to improve the reuse of AI datasets for bioimage analysis” is out in @natmethods.nature.com! Community-driven standards to make bioimage data AI-ready & reusable. 👉 www.nature.com/articles/s41... #AI #Bioimaging #FAIRdata

Better ML for cryo-ET starts with better benchmarks. We built a phantom cryo-ET dataset (~500 tomograms) + hosted a Kaggle challenge. The result: community models beat expert tools. Read more in the @natmethods.nature.com article that just came out: 🔗 doi.org/10.1038/s415...

New Title Alert: DenoisET- an implementation of the Noise2Noise algorithm specifically designed for cryoET data denoising. Learn more here: buff.ly/8i8i87U #SBGrid #SBGridSoftware #StructualBiology

🦠🧠 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 have updated our #MemBrain v2 preprint with a lot more details about the MemBrain-pick and MemBrain-stats modules, as well as some application examples! Stay tuned for the upcoming thread by lead author @lorenzlamm.bsky.social! 🧠🧵 #CryoET #TeamTomo www.biorxiv.org/content/10.1...

Excited to share our preprint on the molecular architecture of heterochromatin in human cells 🧬🔬w/ @jpkreysing.bsky.social, @johannesbetz.bsky.social, @marinalusic.bsky.social, Turoňová lab, @hummerlab.bsky.social @becklab.bsky.social @mpibp.bsky.social 🔗 Preprint here tinyurl.com/3a74uanv

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.

📣 Competition Launch Alert! Locating Bacterial Flagellar Motors 2025 hosted by Brigham Young University. kaggle.com/competitions/byu-locating-bacterial-flagellar-motors-2025

Results from CZII's #cryoET object detection challenge on kaggle are in! Participation exceeded our expectations with 931 Teams from 76 countries competing, generating over 27,000 submissions. For an overview check out our post-competition page: cryoetdataportal.czscience.com/competition

Happy to share our manuscript on the in situ visualization of the copia retrotransposon in its final form today published in @cellcellpress.bsky.social www.cell.com/cell/fulltex.... What’s new?

To all #TeamTomo #CryoET and #Chlamydomonas aficionados: we have updated EMPIAR-11830 with a bug fix concerning some cryo-CARE denoised tomos as well as additional files and metadata! 🎉👩🏽‍💻 www.ebi.ac.uk/empiar/EMPIA... A little thread about what's new... 🧵 1/n

Check out the press release about our recent Nature Methods publication on Segment Anything for Microscopy!

Our first deposition of synaptic vesicles segmentations is now in the Cryo ET Portal! We segmented vesicles in over 50 tomograms to enable analysis of membrane proteins and more. cryoetdataportal.czscience.com/depositions/...

FakET: Simulating cryo-electron tomograms with neural style transfer pubmed.ncbi.nlm.nih.gov/39947174/ #cryoem

Excited to share that Eugene Khvedchenia and I secured 🏆 1st place out of 950 teams in the CryoET Object Identification Competition hosted by the Chan Zuckerberg Institute for Advanced Biological Imaging (CZII) on Kaggle! www.kaggle.com/competitions...

Hey #teamtomo, if you often find yourself using the excellent membrain-seg from @lorenzlamm.bsky.social et al., you might find my napari plugin "napari-segselect" useful. Let's say your tomogram contains the edges of two bacterial cells, each with a membrane and cell wall:

Pranav N. M. Shah et al.: TomoCPT: a generalizable model for 3D particle detection and localization in cryo-electron tomograms ##CryoET##ParticlePicking##SubTomogramAveraging@UniofOxford@IEUniversity...##IUCrhttps://journals.iucr.org/paper?S2059798325000865

And now, support for Zarr v3 & sharding is released as an OME-Zarr specification! 🎉 forum.image.sc/t/ngff-0-5-r... #NGFF #BioImaging #Formats @openmicroscopy.org @zarr.dev

Exciting update on the CryoET Data Portal! A new annotation set from Mart Last & team is now live. They’ve doubled available annotations with >1,800 tomograms of Chlamydomonas reinhardtii which now have almost fully dense labels, and all can be visualized in the browser using Neuroglancer.

I'd like to draw your attention to this truly excellent paper from the Taraska lab on cryoET of plasma membrane associated proteins. Everyone who is thinking about probes in the cryoET space should also see what they could do with ferritag (fig 6) www.nature.com/articles/s41...

Fresh out of the press! ✨Check out our new paper on the violent entry of the HIV capsid into the nuclear pore — and how it cracks the gate! 🤯 💥 Incredible work from @becklab.bsky.social and @hummerlab.bsky.social 🤩 More here: www.biophys.mpg.de/2842024/hivcapsid-cracks-the-npc?c=2011019 🔗 #teamTOMO

Microscopy Nodes is now up on bioRxiv! 🚀 This is a Blender extension that seamlessly integrates and visualizes 3D microscopy data (TIF & @zarr.dev). High-quality volume rendering for anyone, in both EM and fluorescence, regardless of computational expertise! 🔬 www.biorxiv.org/content/10.1...

Looking forward to talking about MemBrain-seg tomorrow and giving a sneak peek into other MemBrain v2 functionalities 👀🚀

Towards community-driven visual proteomics! Excited to finally share this large-scale curated & annotated dataset of 1829 high-quality #cryoET tomograms of the little green alga that just keeps giving— Chlamydomonas! 🧪🧶🧬🌾🌊🌍 Preprint📜: www.biorxiv.org/content/10.1... A short thread🧵👇

Hey #teamtomo checkout our #teamscience approach to #cellbio #cryoET I can’t thank @cellarchlab.com enough for this one 😍😍 Awesome team science from @mpibiochem.bsky.social @biozentrum.bsky.social Thermo Fisher Scientific and more #firstpost on Bluesky www.biorxiv.org/content/10.1...

SPACEtomo v1.2 is online! github.com/eisfabian/SP... - Improved GUIs for lamella detection, target selection and CLEM registration make it the best target selection workflow for PACEtomo on any kind of lamella sample. - Easier installation and configuration Any feedback is much appreciated! :)

Tomorrow(!) morning at 9AM pacific, I am giving a webinar for EMS discussing the surface morphometrics pipeline and our approach to contextual structural biology #teamtomo. Free to attend, hope to see you all there! us06web.zoom.us/webinar/regi...

ChimeraX 1.9 has been released and is available now on our website

Take a look at my personal perspective on the past, present, and future of in situ structural biology with cryo-ET+ While initially skeptical about the genre, I found it fun to write and hopefully, you can enjoy my experiences and some thoughts. Nice weekend y'all www.cambridge.org/core/journal...

New Title Alert: Ais- a tool that provides annotation and segmentation of cryo-ET data using convolutional neural networks. Learn more here: https://buff.ly/4gjsSOu #SBGrid #SBGridSoftware #StructuralBiology

The preview of the @chanzuckerberg.bsky.social Virtual Cell Platform just dropped and there is a nice post about behind the scenes of the CZII CryoET Object Identification challenge: Read more: virtualcellmodels.cziscience.com/benchmark/cr... Participate: cryoetdataportal.czscience.com/competition

Excited to share our new work! We shed light on the sociology of virus-induced condensates supporting reovirus assembly and replication. Visualized using #CryoET #CryoEM and #FIBmilling www.nature.com/articles/s41... Great collab w/ @xianxia13 @zhou_lab Xiaoyu Liu @gonenlab

For the #ML and #CryoET folks out there: Are folks on here submitting to the CZII CryoET Object Identification competition: www.kaggle.com/competitions... ? The leaderboard is really interesting, and the forums are full of insights. How many of the latest picking models have been submitted?

✨𝗡𝗘𝗪 𝗣𝗔𝗣𝗘𝗥 𝗔𝗟𝗘𝗥𝗧✨ We are happy to announce that the paper by Aygul Ishemgulova and members of our group, describing the novel mechanism of cell invasion by enteroviruses is now published in @commsbio.bsky.social ! 🦠 Let’s break it down! 🧵 1/9

Structural biology people: @ucsfchimerax.bsky.social has entered the building.

Proudly present our new preprint on my first post here. We performed SPA on the ciliary tip and identify 7 proteins. Among them, we found the conserved protein SPEF1 at the microtubule seam. In vitro assays show that SPEF1 binds to the seam and stablizes microtubules. www.biorxiv.org/content/10.1...

High-resolution template matching of the human ribosome in situ by Lippincott-Schwartz Lab @hhmijanelia.bsky.social @hhmi.bsky.social. >40 conformations within together reveal molecular dynamics of the elongation cycle with previously unknown bending and “spring-like” motion.

Take a look at our paper from last week where we probed the Molecular Architecture of Synaptic Vesicles by cryo-ET and integrative structural analysis We found that V-ATPases interact with synaptophysin and describe some other molecules of this exciting organelle 🧠🔬❄️ www.pnas.org/doi/10.1073/...

Inaugural post sharing a newly updated version of our little protocol for high quality fiducial removal in #CryoET processing

Anyone have any publicly available data (or data you want to share with me) that you'd love to see segmented? I find myself in need of some fun data to segment in my free time... #cryoET or #volumeEM!

Online @cellpress.bsky.social, we reveal a protein shell that helps diatoms fix 20% of global #CO2 🧪🌊🌾🧶🧬🌍 Shimakawa et al: www.cell.com/cell/fulltex... Nam et al: www.cell.com/cell/fulltex... @biozentrum.bsky.social press release: www.biozentrum.unibas.ch/news/detail/... Read on for more... 1/🧵

A fun journey of full-length EGFR with Dan Leahy and @edwardmarcotte.bsky.social at UT Austin @utaustin.bsky.social. See below: Structure and organization of full-length Epidermal Growth Factor Receptor in extracellular vesicles by cryo-electron tomography www.biorxiv.org/content/10.1...

Really happy to see this one finally online. Great collab with @profmattjohnson.bsky.social @wojwie.bsky.social @lorenzlamm.bsky.social revealing the molecular architecture of grana thylakoids with single-molecule precision inside intact plant chloroplasts! #CryoEM #TeamTomo #PlantScience 🧪🧶🧬🔬🌾

🔊 Exciting AI Research Opportunity! my team at @czbiohub SF is hiring a Research Scientist to develop foundational AI models for BioImage analysis. Join us to work on cutting-edge ML/CV! 💻🔬🧪🧠 #AIJobs #ML job-boards.greenhouse.io/chanzuckerbe...

Faster and more accurate protein modeling with CryFold. By focusing on nearby points (Local Attention) and employing map masking, CryFold excels in generating models from challenging maps regions. It enables a more cost-efficient model building. 🧵 💾 github.com/SBQ-1999/Cry...

First Bluesky post! Our recent eLife paper is now an official version of record. This was my first project using #Cryo-ET and I'm definitely hooked - it's so fun to look at snapshots of synapses within brain tissue and see individual proteins. Excited to share more soon! doi.org/10.7554/eLif...

CZII’s cryoET particle picking machine learning challenge is up and running. More than 3400 signups on Kaggle, great discussions going on, and leaderboard scores better than we were able to do! Start off at: cryoetdataportal.czscience.com/competition

FYI: Thanks to @cellarchlab.com's awesome open science practices, this data is available on the CZ cryoET data portal (dataset 10008) and @ebi.embl.org's EMPIAR (11058)! You can check out the tomograms in your browser here: cryoetdataportal.czscience.com/datasets/10008

If folks aren't aware (especially bioimaging folks), we have a cryoET particle picking competition running (with $$$ prizes): cryoetdataportal.czscience.com/competition We're at >3k entrants with >1k submissions right now. 2 months to go, and the leaderboard is quite interesting already!