uermel.bsky.social - Profile | ThreadSky | a Reddit-style client for Bluesky

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

submitted 5 hours ago • 2 comments

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

submitted 4 days ago • 1 comment

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/...

submitted 7 days ago • 2 comments

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

submitted 14 days ago • 0 comments

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...

submitted 21 days ago • 1 comment

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:

submitted 22 days ago • 2 comments

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...#IUCr https://journals.iucr.org/paper?S2059798325000865

submitted 23 days ago • 0 comments

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

submitted 31 days ago • 0 comments

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.

submitted 36 days ago • 1 comment

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...

submitted 37 days ago • 11 comments

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

submitted 42 days ago • 1 comment

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...

submitted 44 days ago • 9 comments

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

submitted 46 days ago • 1 comment

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🧵👇

submitted 53 days ago • 7 comments

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...

submitted 61 days ago • 2 comments

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! :)

submitted 73 days ago • 0 comments

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...

submitted 74 days ago • 0 comments

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

submitted 77 days ago • 0 comments

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...

submitted 77 days ago • 4 comments

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

submitted 77 days ago • 0 comments

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

submitted 81 days ago • 0 comments

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

submitted 81 days ago • 1 comment

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?

submitted 82 days ago • 0 comments

✨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

submitted 84 days ago • 1 comment

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

submitted 86 days ago • 2 comments

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...

submitted 86 days ago • 1 comment

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.

submitted 87 days ago • 1 comment

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/...

submitted 87 days ago • 1 comment

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

submitted 88 days ago • 0 comments

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!

submitted 89 days ago • 2 comments

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/🧵

submitted 91 days ago • 7 comments

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...

submitted 91 days ago • 6 comments

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 🧪🧶🧬🔬🌾

submitted 93 days ago • 0 comments

🔊 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...

submitted 94 days ago • 1 comment

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...

submitted 95 days ago • 1 comment

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...

submitted 96 days ago • 0 comments

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

submitted 96 days ago • 1 comment

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

submitted 96 days ago • 1 comment

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!

submitted 98 days ago • 0 comments