Utz Ermel
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uermel.bsky.social
Utz Ermel
@uermel.bsky.social
340 followers 680 following 14 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
biohub.org
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... 🧪
natmethods.nature.com Nature Methods @natmethods.nature.com · 3d
Our November issue is now live! 🎉
www.nature.com/nmeth/volume...

On the cover, cell tracking in a developing zebrafish embryo visualized using Ultrack. Cover by Alexandre Dizieux, Jordão Bragantini, Loic Royer, Merlin Lange, CZ Biohub. Paper here: www.nature.com/articles/s41...
November 14, 2025 at 7:23 PM
Reposted by Utz Ermel
evolutionaryscale.bsky.social
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
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.
bit.ly
November 6, 2025 at 6:04 PM
Reposted by Utz Ermel
jcb.org
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/...
November 4, 2025 at 5:30 PM
Reposted by Utz Ermel
aixbiobot.bsky.social
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 1 Figure 2 Figure 3 Figure 4
November 5, 2025 at 10:48 AM
Reposted by Utz Ermel
bioimagearchive.bsky.social
🎉 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
September 15, 2025 at 9:57 AM
Reposted by Utz Ermel
kyleharrington.com
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...
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...
doi.org
August 26, 2025 at 2:22 PM
Reposted by Utz Ermel
sbgrid.bsky.social
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
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.
buff.ly
August 14, 2025 at 4:14 PM
Reposted by Utz Ermel
lorenzlamm.bsky.social
🦠🧠 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
April 25, 2025 at 7:28 AM
Reposted by Utz Ermel
lifeonthewedge.bsky.social
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.
April 23, 2025 at 8:47 AM
Reposted by Utz Ermel
sergiocruzleon.bsky.social
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
April 11, 2025 at 8:35 AM
Reposted by Utz Ermel
florentwaltz.bsky.social
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.
March 21, 2025 at 2:09 PM
Reposted by Utz Ermel
kaggle.com
📣 Competition Launch Alert! Locating Bacterial Flagellar Motors 2025 hosted by Brigham Young University.

kaggle.com/competitions/byu-locating-bacterial-flagellar-motors-2025
BYU - Locating Bacterial Flagellar Motors 2025
Help locate flagellar motors in three-dimensional reconstructions of bacteria.
kaggle.com
March 6, 2025 at 5:20 PM
uermel.bsky.social
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
March 6, 2025 at 5:14 PM
Reposted by Utz Ermel
svenklumpe.bsky.social
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?
March 5, 2025 at 4:02 PM
Reposted by Utz Ermel
lifeonthewedge.bsky.social
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.
February 28, 2025 at 4:35 PM
Reposted by Utz Ermel
cppape.bsky.social
Check out the press release about our recent Nature Methods publication on Segment Anything for Microscopy!
uni-goettingen.de Uni Göttingen @uni-goettingen.de · Feb 24
Automatic cell analysis using #AI

Researchers retrained existing AI-based software on over 17,000 microscopy images with over 2 million structures to develop this new model - Segment Anything for Microscopy: www.uni-goettingen.de/en/3240.html...

#NatureMethods research: doi.org/10.1038/s415...
This is a flat grey image with cell structures in darker grey. Some of the cells are coloured and shown in green boxes. This image - Segmentation of electron microscopy images with μSAM - shows how the model can segment nuclei, with points and boxes from the user and the corresponding masks predicted by the model. Photo: The underlying image comes from data published in Cell (S0092-8674(21)00876-X). Image created by Anwai Archit using the μSAM tool. This is a three dimensional representation with a cross-section showing dark patches in different colours and the outside of the structure with bright different colours (green, purple, blue, dark pink, yellow, orange). The image shows plant cells acquired with a fluorescence microscope that were segmented automatically with the model. The underlying data is three-dimensional and the image shows a rendering of the segmented cells, each represented by a different colour. Image from: Nature Methods: s41592-021-01249-6
February 24, 2025 at 5:27 PM
Reposted by Utz Ermel
cppape.bsky.social
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.
February 21, 2025 at 6:57 AM
Reposted by Utz Ermel
cryoempapers.bsky.social
FakET: Simulating cryo-electron tomograms with neural style transfer pubmed.ncbi.nlm.nih.gov/39947174/ #cryoem
February 14, 2025 at 8:33 PM
Reposted by Utz Ermel
kagglingdieter.bsky.social
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...
February 7, 2025 at 12:48 PM
Reposted by Utz Ermel
bwmr.net
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:
February 6, 2025 at 11:02 AM
Reposted by Utz Ermel
actacrystd.iucr.org
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
TomoCPT: a generalizable model for 3D particle detection and localization in cryo-electron tomograms
TomoCPT is a generalizable transformer-based 3D particle-picking tool for cryo-tomographic data.
journals.iucr.org
February 5, 2025 at 1:00 AM
Reposted by Utz Ermel
joshmoore.bsky.social
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
January 28, 2025 at 3:42 PM
Reposted by Utz Ermel
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.
January 23, 2025 at 8:49 PM
Reposted by Utz Ermel
ritastrack.bsky.social
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...
This is a scientific figure from the paper mentioned in the post. It shows fluorescence and electron microscopy images and associated schematics for using the ferritag to image clathrin coated pit proteins.
January 22, 2025 at 4:40 PM
Reposted by Utz Ermel
mpibp.bsky.social
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
January 17, 2025 at 4:34 PM