Thanks to @uermel.bsky.social from the @biohub.org for helping me upload my unpublished tomograms from my time at Caltech. FIB milled and cryosectionned Arabidopsis cells and Pollen tubes (thread 🧵).

Hello World :) Join us in building foundational subcellular spatial intelligence. To get this party started, we are pleased to announce inaugural call for Subspatial x DECTRIS CLOUD fellowships, apply at subspatial.org/fellowship #subspatial #fellowships #openscience #teamtomo #spatialbiology

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

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)

Excited to share our paper on the NLRP3 inflammasome condensate at the Microtubule Organizing Center (MTOC) by "precise!" cryo-electron tomography (cryo-ET), in collaboration with Jue (phyllis) Wang in the labs of Grant Jensen (BYU) and Pete Dahlberg (Stanford)! www.science.org/doi/10.1126/...

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

#UMAP in VR for #3DThursday! In this zebrafish embryogenesis dataset, RNA-seq + ATAC-seq across 94k+ cells reveal changing regulatory programs over time. 🥼 Yang-Joon Kim, Loic Royer @loicaroyer.bsky.social , Matthias Haury 📝 www.biorxiv.org/content/10.1... 🏛️ Biohub @biohub.org 🎬 #syGlass v2.6.0

New Title Alert: easymode- a collection of general pretrained networks for cellular cryoET. Learn more here: buff.ly/mLbcUbZ #SBGrid #SBGridSoftware

Streaming OME-Zarr data directly into syGlass for #3DThursday🌍🔬 With #syGlass v2.6.0, datasets can stream from disk, S3, or HTTPS with no massive downloads required. Huge thanks to the community building open imaging standards: @openmicroscopy.org #OMEZarr #Microscopy #OpenScience #Bioimaging

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/...

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]

Tired of knowing what you are looking for in your tomograms? Why not try bluesky-less Frosina's new self-supervised algorithm for semantic segmentation and particle picking for #teamtomo (includes a new denoiser without the need for odd/even tomos) Code is on GitHub if you want to try it out

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...

Stunning cover to celebrate the incredible work from @loicaroyer.bsky.social's team. Learn more about Ultrack, a powerful tool for fast, accurate and scalable cell tracking: biohub.org/life-science... 🧪

EvolutionaryScale will be joining forces with Biohub to create the first large-scale scientific initiative combining frontier AI & frontier biology. Together, we're building world-class compute, AI research & state-of-the-art technologies to cure or prevent disease. bit.ly/4nOUGO4

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/...

Lessons learned from a Kaggle challenge for particle picking in cryo-electron tomography [new] Kaggle cryo-ET picking: Over-pick tol, aug, & annot key.

🎉 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?