Lorenz Lamm
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lorenzlamm.bsky.social
Lorenz Lamm
@lorenzlamm.bsky.social
PhD Student at Helmholtz AI | MemBrain analysis for Cryo-ET
#teamTomo
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🦠🧠 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
Reposted by Lorenz Lamm
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
January 30, 2026 at 3:21 PM
Reposted by Lorenz Lamm
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]
January 9, 2026 at 7:15 PM
Reposted by Lorenz Lamm
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...
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]
January 9, 2026 at 7:49 PM
Reposted by Lorenz Lamm
Online Now: Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii Online now:
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.
dlvr.it
December 24, 2025 at 8:14 PM
Reposted by Lorenz Lamm
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
December 3, 2025 at 2:18 AM
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.
December 3, 2025 at 8:25 AM
Reposted by Lorenz Lamm
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
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...
arxiv.org
November 12, 2025 at 12:28 PM
Reposted by Lorenz Lamm
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! 🙏🏽
November 5, 2025 at 2:41 PM
Reposted by Lorenz Lamm
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...
October 21, 2025 at 2:32 PM
Reposted by Lorenz Lamm
✨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...
October 8, 2025 at 3:59 PM
Reposted by Lorenz Lamm
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/🧵
September 25, 2025 at 6:00 PM
Reposted by Lorenz Lamm
🌱 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
September 20, 2025 at 1:59 PM
Reposted by Lorenz Lamm
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 Lorenz Lamm
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
June 17, 2025 at 10:59 AM
Ooh that's awesome! Great to hear the new version improved your segmentations :)
June 16, 2025 at 6:12 PM
Reposted by Lorenz Lamm
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
pytom-match-pick: A tophat-transform constraint for automated classification in template matching pubmed.ncbi.nlm.nih.gov/40475324/ #cryoem
June 9, 2025 at 6:56 AM
Reposted by Lorenz Lamm
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
June 4, 2025 at 4:34 AM
Reposted by Lorenz Lamm
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 !
May 6, 2025 at 4:42 PM
Reposted by Lorenz Lamm
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 🔬🧪
Welcome to TomoGuide
A step-by-step Cryo-ET guide
tomoguide.github.io
May 6, 2025 at 4:27 PM
Reposted by Lorenz Lamm
🚀🔬🦠 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
May 3, 2025 at 7:12 PM
Reposted by Lorenz Lamm
April 22, 2025 at 11:21 PM
Reposted by Lorenz Lamm
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!
🦠🧠 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 10:12 AM
Reposted by Lorenz Lamm
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!
🦠🧠 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 10:25 AM
April 25, 2025 at 7:28 AM
🤝 Feedback
If you feel like trying one of our modules or even the full pipeline, please let us know how it goes. We are happy for any feedback and would love to improve MemBrain v2 even further to make it as helpful for the community as possible.
🧵(6/6)
April 25, 2025 at 7:28 AM