Lorenz Lamm
@lorenzlamm.bsky.social
PhD Student at Helmholtz AI | MemBrain analysis for Cryo-ET
#teamTomo
#teamTomo
Pinned
Lorenz Lamm
@lorenzlamm.bsky.social
· Apr 25
🦠🧠 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
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
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
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
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
So if u fit there, u might wanna check it out! Maybe also if you don't. We're allies here <3
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! 🙏🏽
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
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! 🙏🏽
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! 🙏🏽
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...
napari.org/island-dispa...
October 21, 2025 at 2:32 PM
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...
napari.org/island-dispa...
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...
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
✨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...
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...
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/🧵
#TeamTomo #PlantScience 🧪 🧶🧬 🌾
elifesciences.org/articles/105...
1/🧵
September 25, 2025 at 6:00 PM
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/🧵
#TeamTomo #PlantScience 🧪 🧶🧬 🌾
elifesciences.org/articles/105...
1/🧵
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
buff.ly/j3TSIkn
September 20, 2025 at 1:59 PM
🌱 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
buff.ly/j3TSIkn
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...
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
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...
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...
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
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
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
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
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
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
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
📅 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
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
📅 1 July 9AM CEST
🔗 tinyurl.com/4mjaverj
Spread the word!
@protistwtmostest.bsky.social @ehehenberger.bsky.social @chandnibhickta.bsky.social&Norico Yamada
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 !
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
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 !
You'll find a tutorial on how to reconstruct tomograms, pick particles and do subtomogram averaging, using different software!
Hope it will be useful !
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 🔬🧪
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
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 🔬🧪
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 🔬🧪
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
paper: www.biorxiv.org/content/10.1...
w/ @computingnature.bsky.social 1/n
May 3, 2025 at 7:12 PM
🚀🔬🦠 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
paper: www.biorxiv.org/content/10.1...
w/ @computingnature.bsky.social 1/n
Reposted by Lorenz Lamm
MemBrain v2: an end-to-end tool for the analysis of membranes in cryo-electron tomography [updated]
Cryo-ET membrane analysis via deep learning.
Cryo-ET membrane analysis via deep learning.
April 22, 2025 at 11:21 PM
MemBrain v2: an end-to-end tool for the analysis of membranes in cryo-electron tomography [updated]
Cryo-ET membrane analysis via deep learning.
Cryo-ET membrane analysis via deep learning.
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
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
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!
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
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
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
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
🦠🧠 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
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
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! 🧪🧶🧬🔬
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...
Stay tuned for the upcoming thread by lead author @lorenzlamm.bsky.social! 🧠🧵
#CryoET #TeamTomo
www.biorxiv.org/content/10.1...
April 24, 2025 at 9:35 PM
Reposted by Lorenz Lamm
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...
Stay tuned for the upcoming thread by lead author @lorenzlamm.bsky.social! 🧠🧵
#CryoET #TeamTomo
www.biorxiv.org/content/10.1...
April 23, 2025 at 8:47 AM
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...
Stay tuned for the upcoming thread by lead author @lorenzlamm.bsky.social! 🧠🧵
#CryoET #TeamTomo
www.biorxiv.org/content/10.1...
Reposted by Lorenz Lamm
I've got bad news for #teamtomo: earlier today, our resident headcrab attacked @lorenzlamm.bsky.social, turning his Mem🧠 into 🧟♂️🧠
April 7, 2025 at 8:30 PM
I've got bad news for #teamtomo: earlier today, our resident headcrab attacked @lorenzlamm.bsky.social, turning his Mem🧠 into 🧟♂️🧠
Reposted by Lorenz Lamm
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!🧪🧶🧬🌾
In a new Science study, cryo–electron tomography captures the in-cell architecture of the mitochondrial respiratory chain, illuminating how the coordinated action of molecular machines drives life’s fundamental energy conversion.
Learn more in this week's issue: scim.ag/3FA3Ygq
Learn more in this week's issue: scim.ag/3FA3Ygq
March 20, 2025 at 10:37 PM
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!🧪🧶🧬🌾
Reposted by Lorenz Lamm
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 👩🎨
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 👩🎨
In a new Science study, cryo–electron tomography captures the in-cell architecture of the mitochondrial respiratory chain, illuminating how the coordinated action of molecular machines drives life’s fundamental energy conversion.
Learn more in this week's issue: scim.ag/3FA3Ygq
Learn more in this week's issue: scim.ag/3FA3Ygq
March 20, 2025 at 6:20 PM
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 👩🎨
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 👩🎨
Reposted by Lorenz Lamm
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
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:
Reposted by Lorenz Lamm
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
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.
Reposted by Lorenz Lamm
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.
https://buff.ly/4hutFwf
#SBGridwebinars #ScienceMatters
https://buff.ly/4hutFwf
#SBGridwebinars #ScienceMatters
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...
buff.ly
January 23, 2025 at 6:45 PM
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.
https://buff.ly/4hutFwf
#SBGridwebinars #ScienceMatters
https://buff.ly/4hutFwf
#SBGridwebinars #ScienceMatters