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Utz Ermel

@uermel.bsky.social
428 followers 769 following 28 posts

Scientist at bi[o]hub, Redwood City, CA I like to make open source cryoET things.

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Reposted by Utz Ermel
Ricardo D. Righetto @lifeonthewedge.bsky.social · 08/09/2026
A wild publishing ride to get here... but finally! (first bioRxiv: January 5th, 2024 🙃) Amazing work from @lorenzlamm.bsky.social and colleagues 🤗 Special thanks to the community who jumped early on the boat, sharing feedback and training data to make MemBrain v2 a reality 🙏🏽
nature.com
MemBrain v2: an end-to-end tool for the analysis of membranes in cryo-electron tomography - Nature Methods
MemBrain v2 enables streamlined analysis of membranes in cryo-electron tomography by providing user-friendly tools for membrane segmentation, membrane protein localization and spatial analysis, suppor...
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bioRxiv Molecular Biology @biorxiv-molbio.bsky.social · 28/08/2026
Imaging large fields-of-view at high resolution in cryo-ET with square beam montaging www.biorxiv.org/content/10.64898/20…
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Nature Methods @natmethods.nature.com · 24/08/2026
A Kaggle challenge for particle picking in cryo-ET data spurred the development of new algorithms that outperform state of the art software. www.nature.com/articles/s41...
nature.com
Lessons learned from a Kaggle challenge for particle picking in cryo-electron tomography - Nature Methods
A Kaggle challenge for particle picking in experimental cryo-electron tomography data delivered new machine learning algorithms that outperformed state-of-the-art software and provides a critical refe...
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SBGrid Consortium @sbgrid.bsky.social · 12/08/2026
New Title Alert: copick- is a cross-platform, storage-agnostic & server-less dataset API for cryoET datasets. Access to the data is provided through an object-oriented API that abstracts away the underlying storage using the fsspec-family of libraries. More here: buff.ly/ZBe5Vpd #SBGrid #Software
copick.github.io
Bundled Page
Tools for collaborativecryoET annotation.\n \n\n \n □XY slice · z = {{ depthLabel }}\n \n \n \n \n \n \n \n \n \n…
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Ryan Hylton @rkhylton.bsky.social · 27/07/2026
One cell, one tomogram! Our montage tomography workflow, MOSAIC, is out in Structure, and MontageMaker is on GitHub! MOSAIC: www.cell.com/structure/fu... MontageMaker: github.com/MPI-Dortmund... Big thanks to @maikaboiero.bsky.social, Adriana Prajica, Gavin Rice, and @raunser-lab.bsky.social!
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Laina Hall @lainahall.bsky.social · 25/07/2026
With Cryo-ET/EM, the macromolecules we study (and biological questions we ask) are SNR-limited. Here, we share Nilas, a low-voltage milling method named after thin sea ice. Nilas produces thin (sub 50 nm in places!), minimally damaged lamellae. biorxiv.org/content/10.64898/2026.07.21.739890v1
biorxiv.org
Optimized cryo-FIB milling strategy to generate thin, minimally damaged biological lamellae
Focused ion beam (FIB)-milling has been adapted to thin frozen cells for visualization of macromolecular structures in situ with cryogenic electron microscopy. However, only a few large and abundant c...
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C&EN (Chemical & Engineering News) @cenmag.bsky.social · 24/07/2026
Learn about a device that boosts the contrast in electron microscopy using the most intense laser beam yet made, and the story of its path from an idea to an invention that could open new lines of inquiry in structural biology and biochemistry. #chemsky 🧪
cen.acs.org
Uncovered: Record-setting laser boosts cryo-electron microscopy
Phase-contrast device could allow in-cell proteomics
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Ben Barad @baradlab.com · 08/07/2026
My personal summer of code continues with another ChimeraX plugin - this time, MorphometricsX! Load quantified meshes from morphometrics (or pycurv) in ChimeraX with color-by-quantification and display alongside tomos and particles. Coming to the toolshed soon! #teamtomo github.com/baradlab/mor...
Screenshot of MorphometricsX rendering mitochondrial membrane surfaces in chimera with color-by-quantification.
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Teun Huijben @teunhuijben.bsky.social · 29/06/2026
🚨Open call to the Cell Tracking crowd out there🚨! Loïc's team at @biohub.org opened our Kaggle Challenge for 3D cell tracking, with $60k of prize money💰. Spread the news, delve into our gigabytes of imaging (zarr3) and cell tracking (geff) data of developing zebrafish embryos, and start tracking 🤩
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Marten Chaillet @martenchaillet.bsky.social · 29/06/2026
From v0.2.0 MissAlignment now has an inference mode where you can apply the trained models from one dataset to a new dataset to skip training time. I haven't tested it extensively, so double check if the results look decent 😉 The program calls changed slightly, see here: github.com/warpem/miss-...
github.com
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Ben Barad @baradlab.com · 18/06/2026
Inspired by Utz, I ported the old Briggs lab tools to ChimeraX in a single bundle named Geopickr, with some extra utilities (geopicking on morphometrics surfaces!). I've submitted it to the toolshed, but in the meantime: github.com/baradlab/Geo...
Geopickr enables particle picking on surfaces, spheres, tubes, and filaments interactively in ChimeraX!
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Biohub @biohub.org · 16/06/2026
Cryo-ET gives unparalleled views of cellular structures, but targeted sample preparation by cryo-FIB milling has been a constraint. No longer! A new workflow yields close to 100% targeting success for centrioles & other small structures. Read the preprint ⤵️ www.biorxiv.org/content/10.6...
Diagram of FIB-SEM with integrated fluorescence microscope alongside cryo lamella micrograph and 3D segmentation highlighting targeted centrioles
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Biohub @biohub.org · 11/06/2026
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
Waves of laser light coming from four different directions and meeting in the middle brightly inside the cavity of the laser phase plate
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Utz Ermel @uermel.bsky.social · 11/06/2026
Excited to see POPSICLE out! 🍦 A combined benchmark for cryoET and evaluations with common segmentation models. Find the full dataset here: huggingface.co/datasets/bio...
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Markus Schreiber @ms314.bsky.social · 28/05/2026
We have published a review on how contextual information can complement and enhance research using #cryoET . www.sciencedirect.com/science/arti...
sciencedirect.com
Context matters: A view on metadata analysis in cryo-electron tomography
Cryo-electron tomography (cryo-ET) enables the analysis of biological samples in situ, revealing the complex interplay that shapes (sub)cellular archi…
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Biohub @biohub.org · 27/05/2026
Proteins are the machinery of life. Billions of their sequences have been cataloged—but the biology behind most is still unknown. Today we're releasing ESMFold2, ESMC and ESM Atlas to help change that. Open source, open to every scientist. biohub.ai/esm/protein
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Allegretti Lab @matteoall.bsky.social · 27/05/2026
We're happy to announce our new preprint! 🐸 easymode: general pretrained networks for cellular cryo-ET. Segment ~20 cellular features – ribosomes, microtubules, mitochondria, nuclei & more – with zero model training. 🔗 doi.org/10.64898/202... 🧵👇
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Martin Panknin @mpanknin.bsky.social · 26/05/2026
Volumetric exploration of multi-resolution CryoET data in native WebGPU. Kiln (0.3.0) adds float32 support, OME-Zarr v0.4, slice views and more. github.com/MPanknin/kil... Vibrio cholerae tomogram from CryoET Data Portal. cryoetdataportal.czscience.com #WebGPU #OME-Zarr #CryoET
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cryoEM papers @cryoempapers.bsky.social · 22/05/2026
Easymode: general pretrained networks for cellular cryo-ET enable flexible approaches to subtomogram averaging www.biorxiv.org/content/10.64898/2026.05.19.726344v1 #cryoEM
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William J Nicolas @wjnicol.bsky.social · 09/05/2026
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 🧵).
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Subspatial @subspatial.org · 02/05/2026
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
subspatial.org
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Biohub @biohub.org · 29/04/2026
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
bit.ly
Biohub launches the Virtual Biology Initiative
A $500M commitment to galvanize a global, open-data effort to build predictive models of the human cell.
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Helena Watson @helenawatson.bsky.social · 25/04/2026
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)
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Prof. Hao Wu @wulabharvard.bsky.social · 23/04/2026
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/...
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Utz Ermel @uermel.bsky.social · 20/04/2026
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
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Brandy A Freitas @brandy-syglass.bsky.social · 09/04/2026
#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
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SBGrid Consortium @sbgrid.bsky.social · 13/03/2026
New Title Alert: easymode- a collection of general pretrained networks for cellular cryoET. Learn more here: buff.ly/mLbcUbZ #SBGrid #SBGridSoftware
buff.ly
easymode
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Brandy A Freitas @brandy-syglass.bsky.social · 12/03/2026
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
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Utz Ermel @uermel.bsky.social · 27/01/2026
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/...
Four representative slices of cryo-tomograms showing annotated organelles.
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Ricardo D. Righetto @lifeonthewedge.bsky.social · 09/01/2026
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]
cell.com
Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii
Using the latest advances in instrumentation and computational workflows, Kelley et al. present a large-scale annotated cryo-electron tomography dataset of the model green alga, Chlamydomonas reinhard...
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Rasmus Jensen @rasmusjensen.bsky.social · 19/11/2025
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
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Utz Ermel @uermel.bsky.social · 17/11/2025
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...
github.com
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
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Biohub @biohub.org · 14/11/2025
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... 🧪
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EvolutionaryScale @evolutionaryscale.bsky.social · 06/11/2025
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
bit.ly
Biohub launches initiative combining frontier AI & frontier biology
The large-scale scientific effort combines frontier AI with frontier biology to accelerate discovery and solve disease.
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Journal of Cell Biology @jcb.org · 04/11/2025
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/...
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AI x Bio Discovery @aixbiobot.bsky.social · 05/11/2025
Lessons learned from a Kaggle challenge for particle picking in cryo-electron tomography [new] Kaggle cryo-ET picking: Over-pick tol, aug, & annot key.
Figure 1Figure 2Figure 3Figure 4
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The BioImage Archive @bioimagearchive.bsky.social · 15/09/2025
🎉 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
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Kyle Harrington @kyleharrington.com · 26/08/2025
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...
doi.org
A realistic phantom dataset for benchmarking cryo-ET data annotation - Nature Methods
A standardized, realistic phantom dataset consisting of ground-truth annotations for six diverse molecular species is provided as a community resource for cryo-electron-tomography algorithm benchmarki...
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SBGrid Consortium @sbgrid.bsky.social · 14/08/2025
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
buff.ly
GitHub - apeck12/denoiset: An implementation of Noise2Noise for cryoET data
An implementation of Noise2Noise for cryoET data. Contribute to apeck12/denoiset development by creating an account on GitHub.
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Lorenz Lamm @lorenzlamm.bsky.social · 25/04/2025
🦠🧠 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
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Ricardo D. Righetto @lifeonthewedge.bsky.social · 23/04/2025
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...
Figure 4. MemBrain v2 end-to-end workflow detects periodic phycobilisome organization. A: Raw tomogram slice of EMD-31244. B: Out-of-the-box MemBrain-seg segmentation (light blue). C: A single membrane instance can be visualized in Surforama and manually annotated with GT phycobilisome positions (magenta). D: MemBrain-pick localizes particles (trained with data from C) on all membranes in the tomogram. E: MemBrain-stats computes Ripley’s O statistic using the positions from D with a bin size of 5nm. The distance between peaks (35 nm) was measured to estimate chain unit spacings.
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Sergio Cruz-León @sergiocruzleon.bsky.social · 11/04/2025
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
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Florent Waltz @florentwaltz.bsky.social · 21/03/2025
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.
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Kaggle @kaggle.com · 06/03/2025
📣 Competition Launch Alert! Locating Bacterial Flagellar Motors 2025 hosted by Brigham Young University. kaggle.com/competitions/byu-locating-bacterial-flagellar-motors-2025
kaggle.com
BYU - Locating Bacterial Flagellar Motors 2025
Help locate flagellar motors in three-dimensional reconstructions of bacteria.
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Utz Ermel @uermel.bsky.social · 06/03/2025
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
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Sven Klumpe @svenklumpe.bsky.social · 05/03/2025
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?
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Ricardo D. Righetto @lifeonthewedge.bsky.social · 28/02/2025
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
Rare cellular events observed in the cryo-ET dataset. Slices through tomograms (left) with corresponding 3D segmentation (middle and right). Right panels show enlarged views of the boxed regions in the middle panels. A) Mitochondrion at the plasma membrane, tethered to microtubules by thin filaments of unknown identity. Segmented classes: nuclear envelope (light blue), nuclear pore complex (dark blue), 80S ribosomes (orange), mitochondrial membranes (dark red), ATP synthase (royal blue), plasma membranes (grey), microtubules (pink), filaments (yellow), endoplasmic reticulum (purple). Zoomed-in panel shows thin filaments running between microtubules and the mitochondrion at the plasma membrane. Note that this tomogram contains two closely appressed cells, and thus, two plasma membranes with cell walls between. B) Mitochondrial fission event with ER membrane interactions. Segmented classes: mitochondrial membranes (dark red), ATP synthase (royal blue), 80S ribosomes (orange), thylakoid membranes (green), PSII (bright yellow), cell wall (grey), ER (purple), fission site containing filamentous structures perpendicular to the mitochondrial long axis (pale yellow). C) Ciliary transition zone between basal body and axoneme, including assembling IFT train and stellate structure77. Segmented classes: microtubule doublets (light blue), central microtubule pair (light green), stellate structure (pale red), IFT train (yellow). D) Pyrenoid tubule extending from the thylakoids into the phase-separated Rubisco matrix of the pyrenoid. Minitubules originate from thylakoid membranes82. Segmented classes: thylakoid membranes (dark green), PSII (yellow), pyrenoid tubule (lime green), Rubisco (lavender blue), minitubules (orange). Scale bars in A-D: 100 nm. Related to Fig. 2C-H.
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Constantin Pape @cppape.bsky.social · 24/02/2025
Check out the press release about our recent Nature Methods publication on Segment Anything for Microscopy!
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Constantin Pape @cppape.bsky.social · 21/02/2025
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/...
Synaptic vesicles segmented with SynapseNet.
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cryoEM papers @cryoempapers.bsky.social · 14/02/2025
FakET: Simulating cryo-electron tomograms with neural style transfer pubmed.ncbi.nlm.nih.gov/39947174/ #cryoEM
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