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Lorenz Lamm

@lorenzlamm.bsky.social
260 followers 307 following 13 posts

PhD Student at Helmholtz AI | MemBrain analysis for Cryo-ET #teamTomo

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Reposted by Lorenz Lamm
Mihris Naduthodi @mihrisn.bsky.social · 22/07/2026
(1/16) Nearly two-thirds of ocean carbon fixation flows through a diverse organelle: the pyrenoid. Our new paper maps its 3D architecture in the alga Chlorella and identifies new proteins — expanding the toolkit to engineer this CO2-concentrating machine into crops🧵 #Pyrenoid #CCM #Photosynthesis
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Ben Engel @cellarchlab.com · 22/07/2026
It’s a pyrenoid party! 🪩🌍 Awesome collab🤝 of @phaips.vd.st & @manondemulder.bsky.social with Mihris and the @mackinderlab.bsky.social crew to reveal the molecular architecture🏗️ of the Chorella pyrenoid. Algae have so many convergently evolved compartments to supercharge #CO2 capture. #TeamTomo 🔬🌾🌊🧪
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Kathiravan Ezhilan @kathiravan-ezhilan.bsky.social · 16/07/2026
In #cryoET, separating closely apposed membrane segmentations into distinct labels can be difficult. Small artefacts may connect otherwise separate membranes, requiring tedious slice-by-slice correction. To address this, @jasmred.bsky.social and I developed MemSplit, a napari based workflow.
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Dimitry Tegunov @dtegunov.bsky.social · 03/05/2026
We're super excited to share MissAlignment: a new ML-based approach to reference-free tilt series alignment, spearheaded by @martenchaillet.bsky.social. We think it's going to make your cryo-ET life a lot better. Preprint: www.biorxiv.org/content/10.6... Code: github.com/warpem/miss-... 🧶 Thread:
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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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Florent Waltz @florentwaltz.bsky.social · 10/02/2026
Long in the making, but happy to present the Chlamydomonas chlororibosome! Cryo-ET🔬reveals a large new domain on the small subunit, built from multiple extensions in conserved ribosomal proteins. bioRxiv 📖: shorturl.at/q44tG This suggests greater chlororibosome diversity than expected! 1/n 🧵
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James Barrett @james-r-barrett.bsky.social · 30/01/2026
How does molecular valency shape condensate assembly and function? We used the CO2-fixing organelle in algae—the pyrenoid—to find out… 🧵 Preprint here!: www.biorxiv.org/content/10.6... @cellarchlab.com @phaips.vd.st @biologyatyork.bsky.social #Rubisco #PhaseSeparation #Condensates #Pyrenoid
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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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Ben Engel @cellarchlab.com · 09/01/2026
The #ChlamyDataset is on the cover of @cp-molcell.bsky.social 🖼️🥰! Read @lifeonthewedge.bsky.social's great thread🧵 for the inside scoop🍨 on all the #TeamTomo developments already made possible since these 1829 tomos hit EMPIAR 🧪 🧶🧬 For more, here's the old preprint thread: bsky.app/profile/cell...
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Molecular Cell @cp-molcell.bsky.social · 24/12/2025
Online Now: Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii Online now:
dlvr.it
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 reinhardtii. This unprecedented community resource is rich in high-resolution biological information and empowers the development of new methods for visual proteomics.
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Joel Valdivia Ortega @virtualhomo.bsky.social · 03/12/2025
In case you're missing my poster at #NeurIPS2025 about how I fine-tuned DINOv2 to ophthalmological images, here are some animations so you don't miss out! 🔗 Preprint: doi.org/10.48550/arX... 🔗 Code: github.com/peng-lab/rmlp 🧵1/9
Attention maps and PCA visualisations comparing mode
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Lorenz Lamm @lorenzlamm.bsky.social · 03/12/2025
Are you also often frustrated when DINOv2 puts very high attention on background patches, rather than cute fox heads? @virtualhomo.bsky.social found an elegant way to regularize DINOv2 training using randomised linear algebra 🤯 Check out his thread or even his poster if you're at #NeurIPS2025.
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Joel Valdivia Ortega @virtualhomo.bsky.social · 12/11/2025
I wrote a paper with @lorenzlamm.bsky.social, @marionjasnin.bsky.social, @tingyingpeng.bsky.social, F. Eckardt and B. Schworm and got accepted at #NeurIPS2025 and fun fact: 90% of viewers are enby vegans! 🤟 So if u fit there, u might wanna check it out! Maybe also if you don't. We're allies here <3
arxiv.org
Randomized-MLP Regularization Improves Domain Adaptation and Interpretability in DINOv2
Vision Transformers (ViTs), such as DINOv2, achieve strong performance across domains but often repurpose low-informative patch tokens in ways that reduce the interpretability of attention and feature...
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Ricardo D. Righetto @lifeonthewedge.bsky.social · 05/11/2025
I'm pleased to announce 🍦 Icecream 🍨 v0.3! New features include: * Training on multiple tomograms (same training time, with linear increase in RAM) 🚀 * Logging and plotting of the loss function 📉 * The --scale option is now called --eq-weight for clarity 😉 We'd love to hear your feedback! 🙏🏽
github.com
GitHub - swing-research/icecream: 🍦Icecream: a self-supervised framework for cryo-ET reconstruction
🍦Icecream: a self-supervised framework for cryo-ET reconstruction - swing-research/icecream
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napari @napari.org · 21/10/2025
You might have noticed lots of activity in the napari project recently! 🚀 We're grateful for a grant from CZI that's keeping us going, but grants don't last forever: we're trying to figure out sustainable long term funding. Read our blog post to find out how you can help: napari.org/island-dispa...
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Kenneth Ehses @denkenny.bsky.social · 08/10/2025
✨Excited that the main project of my PhD is now available as a pre-print on #bioRxiv Here, we used #CryoET to visualise mitochondrial proteostatic stress and together with SPA #CryoEM shed light into the functional cycle of the Hsp60:10 chaperone system. #TeamTomo 🔗 www.biorxiv.org/content/10.1...
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Ben Engel @cellarchlab.com · 25/09/2025
Time for a thread!🧵 How different is the molecular organization of thylakoids in “higher” plants🌱? To find out, we teamed up with @profmattjohnson.bsky.social to dive into spinach chloroplasts with #CryoET ❄️🔬. Curious? ..Read on! #TeamTomo #PlantScience 🧪 🧶🧬 🌾 elifesciences.org/articles/105... 1/🧵
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eLife @elife.bsky.social · 20/09/2025
🌱 Using ‘compelling’ methods, including #CryoET, researchers mapped spinach thylakoid membranes at single-molecule precision, revealing how photosynthetic complexes are organised and settling long-standing debates on chloroplast architecture. buff.ly/j3TSIkn
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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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Michael Grange @michaelgrange.bsky.social · 17/06/2025
Proud to share our latest paper. doi.org/10.1016/j.cr... Through the dedication of @glynnca.bsky.social and @cryingem.bsky.social we report a thorough method to image molecular organisation within hippocampus tissue. Structural biology in tissue is well and truly here! @rosfrankinst.bsky.social
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Marten Chaillet @martenchaillet.bsky.social · 09/06/2025
Final PhD paper now reviewed and published in JSB:X. I was happy with some great reviews that improved the paper! Thanks to Sander Roet for his help with the code base, and Remco Veltkamp and @fridof.bsky.social
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Manon Demulder @manondemulder.bsky.social · 04/06/2025
We’re kicking off the DinoSphere Online Seminar Series! Join us for our first session with Karel Mockaer (Heidelberg) & Yong Heng Phua (OIST) 📅 1 July 9AM CEST 🔗 tinyurl.com/4mjaverj Spread the word! @protistwtmostest.bsky.social @ehehenberger.bsky.social @chandnibhickta.bsky.social&Norico Yamada
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Florent Waltz @florentwaltz.bsky.social · 06/05/2025
You want to start tomography? Solve structures inside cells? Reach Nyquist 😳 ? @phaips.vd.st and I have a website for you! tomoguide.github.io You'll find a tutorial on how to reconstruct tomograms, pick particles and do subtomogram averaging, using different software! Hope it will be useful !
3.8 angstrom resolution ribosome from 33 tomograms The TomoGuide website
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Philippe Van der Stappen @phaips.vd.st · 06/05/2025
Hey #TeamTomo, Ever been in need of a tutorial about the fundamentals of cryo-electron tomography? From preprocessing raw frames to high-res subtomogram averaging? That's why @florentwaltz.bsky.social and I made this website! tomoguide.github.io Follow the thread 1 /🧵 #CryoET #CryoEM 🔬🧪
tomoguide.github.io
Welcome to TomoGuide
A step-by-step Cryo-ET guide
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Marius Pachitariu @marius10p.bsky.social · 03/05/2025
🚀🔬🦠 Releasing 🤖Cellpose-SAM🤖, a cellular segmentation algorithm with superhuman generalization 🦸‍♀️. Try it now on 🤗 huggingface.co/spaces/mouse... paper: www.biorxiv.org/content/10.1... w/ @computingnature.bsky.social 1/n
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AI x Bio Discovery @aixbiobot.bsky.social · 23/04/2025
MemBrain v2: an end-to-end tool for the analysis of membranes in cryo-electron tomography [updated] Cryo-ET membrane analysis via deep learning.
MemBrain v2: an end-to-end tool for the analysis of membranes in cryo-electron tomographyFigure 1Figure 2Figure 3
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Tingying Peng @tingyingpeng.bsky.social · 25/04/2025
We’ve updated our powerful MemBrain-seg tool for CryoET membrane segmentation! Plus, we’re introducing two new tools: MemBrain-pick for particle picking and MemBrain-stats for statistical analysis. Feedback is warmly welcome!
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Florent Waltz @florentwaltz.bsky.social · 25/04/2025
Check out the latest version of MemBrain, spearheaded by computation superstar @lorenzlamm.bsky.social ! It can segment, pick particles and give you metrics on everything!
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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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Ben Engel @cellarchlab.com · 24/04/2025
Yo #TeamTomo, check out our updated #MemBrain v2 preprint. And better yet, give it a whirl on your #CryoET membranes! Please send us your feedback! 🧪🧶🧬🔬
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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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Dimitry Tegunov @dtegunov.bsky.social · 07/04/2025
I've got bad news for #teamtomo: earlier today, our resident headcrab attacked @lorenzlamm.bsky.social, turning his Mem🧠 into 🧟‍♂️🧠
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Ben Engel @cellarchlab.com · 20/03/2025
We're on the cover of @science.org this week. Awesome work by @florentwaltz.bsky.social. #CryoET is reaching crazy resolutions inside cells, and this is just the beginning. Fantastic interpretation of the proton motive force by @verenaresch.bsky.social. Always a pleasure making #SciArt with you!🧪🧶🧬🌾
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Florent Waltz @florentwaltz.bsky.social · 20/03/2025
The final version of our work on the in-cell architecture of the mitochondrial respiratory chain is now online in @science.org 🎉 You can find the full story here www.science.org/doi/10.1126/... @verenaresch.bsky.social did a wonderful job on the cover and animation, she really brought it to life 👩‍🎨
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Benedikt Wimmer @bwmr.net · 06/02/2025
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:
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Bridget Carragher @bcarra.bsky.social · 23/01/2025
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.
cryoetdataportal.czscience.com
CryoET Data Portal
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SBGrid Consortium @sbgrid.bsky.social · 23/01/2025
In case you missed our first webinar of 2025, it is now available. Lorenz Lamm from MUDS - Munich School for Data Science presented MemBrainv2- an end-to-end tool for the analysis of membranes in cryo-electron tomography. buff.ly/4hutFwf #SBGridwebinars #ScienceMatters
buff.ly
MemBrainv2
SBGrid webinars are hosted with partial support from the NIH R25 Continuing Education for Structural Biology Mentors #GM151273, in collaboration with Co-PI J...
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Lorenz Lamm @lorenzlamm.bsky.social · 13/01/2025
Looking forward to talking about MemBrain-seg tomorrow and giving a sneak peek into other MemBrain v2 functionalities 👀🚀
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Ben Engel @cellarchlab.com · 06/01/2025
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🧵👇
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Philippe Van der Stappen @phaips.vd.st · 29/12/2024
More than 1'800 tomograms available for the community. Towards visual proteomics using our favorite organism Chlamy! Check out the preprint: www.biorxiv.org/content/10.1... Find it on EMPIAR (11830) and fully annotated on the CZI data portal: cryoetdataportal.czscience.com #TeamTomo
biorxiv.org
Towards community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii
In situ cryo-electron tomography (cryo-ET) has emerged as the method of choice to investigate structures of biomolecules in their native context. However, challenges remain in the efficient production...
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Ben Engel @cellarchlab.com · 29/12/2024
I’ll have more to say about this later, but please have a look, and I hope the #TeamTomo community finds good uses for those 1829 Chlamy tomograms 🧪🧶🧬🌾🔬
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Sagar Khavnekar @cryosagar.subspatial.org · 29/12/2024
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...
biorxiv.org
Towards community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii
In situ cryo-electron tomography (cryo-ET) has emerged as the method of choice to investigate structures of biomolecules in their native context. However, challenges remain in the efficient production...
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Julia Schnabel @ja-schnabel.bsky.social · 09/12/2024
Annual #MuDS Munich School of Data Science PhD retreat on Frauenchiemsee - scientific talks, posters & networking by our fabulous PhDs at @www.helmholtz-munich.de @tu-munich.bsky.social #LMU - set in the lovely monastery Frauenwörth, originally founded in 782 (!) on this lovely Chiemsee island
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sofie.rec @sofie-dot-rec.bsky.social · 27/11/2024
Check out @wojwie.bsky.social and @lorenzlamm.bsky.social work on the thylakoid membranes in spinach! Wojciech stared to long at the segmentations and started seeing Van Goghs in it, so we made his fever dream a reality. More work from #teamthylakoid to come under the starry night skies of Basel!
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Ben Engel @cellarchlab.com · 27/11/2024
It took us seven years, but our collaboration with @profmattjohnson.bsky.social on the molecular architecture of plant thylakoids is finally online. Check it out! #PlantScience #TeamTomo 🧪🔬🧶🧬🌾
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Matt Johnson @profmattjohnson.bsky.social · 27/11/2024
🥳New cryo tomography Preprint ☀️🌱🔬Molecular architecture of thylakoid membranes within intact spinach chloroplasts. doi.org/10.1101/2024.1… Proud to be part of this great work with @cellarchlab.com @wojwie.bsky.social @sheffieldpps.bsky.social
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Ben Engel @cellarchlab.com · 27/11/2024
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 🧪🧶🧬🔬🌾
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woj_wie @wojwie.bsky.social · 27/11/2024
This one was delayed for a while… apologies to the musicians. Collab with Matt, Will and Lorna (over on Twitter). And a great dev effort from Lorenz @lorenzlamm.bsky.social. Ofc @cellarchlab.com team. Comment if you want to help. #teamthylakoid www.biorxiv.org/content/10.1...
biorxiv.org
Molecular architecture of thylakoid membranes within intact spinach chloroplasts
Thylakoid membranes coordinate the light reactions of photosynthesis across multiple scales, coupling the architecture of an elaborate membrane network to the spatial organization of individual protei...
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Utz Ermel @uermel.bsky.social · 24/11/2024
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
cryoetdataportal.czscience.com
Cryo-electron tomograms of T. kivui of FIB-SEM lamella.
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