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...
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/...
cryoetdataportal.czscience.com/depositions/...
January 27, 2026 at 7:59 PM
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/...
cryoetdataportal.czscience.com/depositions/...
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!
Looking forward to talking about MemBrain-seg tomorrow and giving a sneak peek into other MemBrain v2 functionalities 👀🚀
On January 14th, our software webinar will feature @lorenzlamm.bsky.social , MUDS - Munich School for Data Science Fellow at Boehringer Ingelheim, on MemBrain v2.
MemBrain v2
Tuesday, January 14, 2025 at 12:00pm EDT
Lorenz Lamm
Register here: https://buff.ly/36OEPwR
#structuralbiology #webinars
MemBrain v2
Tuesday, January 14, 2025 at 12:00pm EDT
Lorenz Lamm
Register here: https://buff.ly/36OEPwR
#structuralbiology #webinars
Webinars
The SBGrid Consortium is an innovative global research computing group operated out of Harvard Medical School. SBGrid provides the global structural biology community with support for research…
buff.ly
January 13, 2025 at 5:33 PM
Looking forward to talking about MemBrain-seg tomorrow and giving a sneak peek into other MemBrain v2 functionalities 👀🚀
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:
I am getting excited about teaching at this! I think we're going to do copick, membrain-seg, morphometrics, and surforama on my day!
Join us this summer for U-M's 2026 #CryoET Data Processing Workshop!
This four-day workshop will introduce participants to standard image processing packages and all aspects of cryo-ET data processing.
Apply by March 20: myumi.ch/lsi-cryo-workshop-2026
@jbquerido.bsky.social @shyamalm.bsky.social
This four-day workshop will introduce participants to standard image processing packages and all aspects of cryo-ET data processing.
Apply by March 20: myumi.ch/lsi-cryo-workshop-2026
@jbquerido.bsky.social @shyamalm.bsky.social
February 11, 2026 at 4:32 AM
I am getting excited about teaching at this! I think we're going to do copick, membrain-seg, morphometrics, and surforama on my day!
Our #TeamTomo adventure continues! 🔬
Here is Bob's first attempt running MemBrain-seg on one of his tomograms 😍
@bobcoelingh.bsky.social
Here is Bob's first attempt running MemBrain-seg on one of his tomograms 😍
@bobcoelingh.bsky.social
November 9, 2023 at 12:32 PM
Our #TeamTomo adventure continues! 🔬
Here is Bob's first attempt running MemBrain-seg on one of his tomograms 😍
@bobcoelingh.bsky.social
Here is Bob's first attempt running MemBrain-seg on one of his tomograms 😍
@bobcoelingh.bsky.social
New Title Alert: MemBrain-v2- is a tool that includes MemBrain-seg, MemBrain-pick, MemBrain-stats, and several Napari tools.
Learn more here: buff.ly/U3s12Ic
#SBGrid #SBGridSoftware
Learn more here: buff.ly/U3s12Ic
#SBGrid #SBGridSoftware
CellArchLab/MemBrain-v2
This is the main repository for MemBrain v2. It includes MemBrain-seg, MemBrain-pick, MemBrain-stats, and several Napari tools. - CellArchLab/MemBrain-v2
buff.ly
April 10, 2026 at 4:05 PM
New Title Alert: MemBrain-v2- is a tool that includes MemBrain-seg, MemBrain-pick, MemBrain-stats, and several Napari tools.
Learn more here: buff.ly/U3s12Ic
#SBGrid #SBGridSoftware
Learn more here: buff.ly/U3s12Ic
#SBGrid #SBGridSoftware
For a starter, #MemBrain-seg from @lorenzlamm.bsky.social would not have been possible without the #ChlamyDataset and lots of other kind contributions from the #CryoET community 🙏🏽
#TeamTomo
#TeamTomo
🦠🧠 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
January 9, 2026 at 7:15 PM
For a starter, #MemBrain-seg from @lorenzlamm.bsky.social would not have been possible without the #ChlamyDataset and lots of other kind contributions from the #CryoET community 🙏🏽
#TeamTomo
#TeamTomo
⚖️ MemBrain-stats
This module analyzes the spatial organization of particles on membranes. It takes the outputs of MemBrain-seg and MemBrain-pick to compute metrics like particle concentrations and geodesic nearest neighbor distances.
🧵(4/6)
This module analyzes the spatial organization of particles on membranes. It takes the outputs of MemBrain-seg and MemBrain-pick to compute metrics like particle concentrations and geodesic nearest neighbor distances.
🧵(4/6)
April 25, 2025 at 7:28 AM
⚖️ MemBrain-stats
This module analyzes the spatial organization of particles on membranes. It takes the outputs of MemBrain-seg and MemBrain-pick to compute metrics like particle concentrations and geodesic nearest neighbor distances.
🧵(4/6)
This module analyzes the spatial organization of particles on membranes. It takes the outputs of MemBrain-seg and MemBrain-pick to compute metrics like particle concentrations and geodesic nearest neighbor distances.
🧵(4/6)
🔑 Usability
We focused on making MemBrain v2 smooth to work with: MemBrain-seg works with a single command line, while MemBrain-pick enables data-efficient training. We facilitate the transition between modules with several Napari functionalities like the 3D lasso to crop areas of interest.
🧵(5/6)
We focused on making MemBrain v2 smooth to work with: MemBrain-seg works with a single command line, while MemBrain-pick enables data-efficient training. We facilitate the transition between modules with several Napari functionalities like the 3D lasso to crop areas of interest.
🧵(5/6)
April 25, 2025 at 7:28 AM
🔑 Usability
We focused on making MemBrain v2 smooth to work with: MemBrain-seg works with a single command line, while MemBrain-pick enables data-efficient training. We facilitate the transition between modules with several Napari functionalities like the 3D lasso to crop areas of interest.
🧵(5/6)
We focused on making MemBrain v2 smooth to work with: MemBrain-seg works with a single command line, while MemBrain-pick enables data-efficient training. We facilitate the transition between modules with several Napari functionalities like the 3D lasso to crop areas of interest.
🧵(5/6)
One of my favorite applications: Desislava Glushkova, Stefanie Böhm and Martin Beck have used #MemBrain-seg and this dataset to show systematic membrane thickness variations across organelles 📏
Just published! We share an open-source workflow to measure membrane thickness from tomograms, including a tutorial with 3D visualizations. We analyze thickness variations across organelles and reflect on where to define a membrane boundary. @becklab.bsky.social #teamtomo rupress.org/jcb/article/...
January 9, 2026 at 7:15 PM
One of my favorite applications: Desislava Glushkova, Stefanie Böhm and Martin Beck have used #MemBrain-seg and this dataset to show systematic membrane thickness variations across organelles 📏
🎨 MemBrain-seg
This module allows out-of-the-box segmentation of membranes with just a single command line.
It’s based on a U-Net architecture, trained with a diverse dataset to enable generalization to many settings.
🔗 github.com/teamtomo/mem...
🧵(2/6)
This module allows out-of-the-box segmentation of membranes with just a single command line.
It’s based on a U-Net architecture, trained with a diverse dataset to enable generalization to many settings.
🔗 github.com/teamtomo/mem...
🧵(2/6)
April 25, 2025 at 7:28 AM
🎨 MemBrain-seg
This module allows out-of-the-box segmentation of membranes with just a single command line.
It’s based on a U-Net architecture, trained with a diverse dataset to enable generalization to many settings.
🔗 github.com/teamtomo/mem...
🧵(2/6)
This module allows out-of-the-box segmentation of membranes with just a single command line.
It’s based on a U-Net architecture, trained with a diverse dataset to enable generalization to many settings.
🔗 github.com/teamtomo/mem...
🧵(2/6)
You can find the plugin on napari-hub here: www.napari-hub.org/plugins/napa...
and the GitHub repository here: github.com/bwmr/napari-...
and the GitHub repository here: github.com/bwmr/napari-...
SegSelect - napari Plugin - Benedikt Wimmer
Select a connected component from a membrain-seg segmentation.
www.napari-hub.org
February 6, 2025 at 11:02 AM
You can find the plugin on napari-hub here: www.napari-hub.org/plugins/napa...
and the GitHub repository here: github.com/bwmr/napari-...
and the GitHub repository here: github.com/bwmr/napari-...
In all seriousness, the development model there has evolved continuously and there have been growing pains! membrain-seg with @lifeonthewedge.bsky.social @lorenzlamm.bsky.social @cellarchlab.com was our first time trying to include others and that experience informed the way things look today :-)
September 16, 2025 at 7:17 PM
In all seriousness, the development model there has evolved continuously and there have been growing pains! membrain-seg with @lifeonthewedge.bsky.social @lorenzlamm.bsky.social @cellarchlab.com was our first time trying to include others and that experience informed the way things look today :-)
New Title Alert: Napari-SegSelect- is a plugin for Napari to select a connected component from a Membrain-seg segmentation.
Learn more here: buff.ly/q1RPNud
#SBGrid #SBGridSoftware
Learn more here: buff.ly/q1RPNud
#SBGrid #SBGridSoftware
SegSelect - napari Plugin - Benedikt Wimmer
Select a connected component from a membrain-seg segmentation.
buff.ly
April 15, 2026 at 4:05 PM
New Title Alert: Napari-SegSelect- is a plugin for Napari to select a connected component from a Membrain-seg segmentation.
Learn more here: buff.ly/q1RPNud
#SBGrid #SBGridSoftware
Learn more here: buff.ly/q1RPNud
#SBGrid #SBGridSoftware
Technical Notes: October's software push includes updates to cryoDRGN, CryoSieve, cyrosparc-tools, DIALS, MemBrain-Seg, PHYLIP, qFit, ShelXle, and Warp.
More here:
More here:
SBGrid Consortium - Software Updates
The SBGrid Consortium is an innovative global research computing group operated out of Harvard Medical School. SBGrid provides the global structural biology community with support for research…
buff.ly
November 8, 2024 at 5:00 PM
Technical Notes: October's software push includes updates to cryoDRGN, CryoSieve, cyrosparc-tools, DIALS, MemBrain-Seg, PHYLIP, qFit, ShelXle, and Warp.
More here:
More here:
Technical Updates: Our May software push includesd updates to 21 titles including bedtools, cryosparc-tools, cryoDRGN, deepTools, DIALS, EMReady, IMP, IMOD, Jalview, IGV, MemBrain-Seg, MGLTools, PEET, Phenix, POKY, PyMOL, R, RStudio, Relion, Rosetta, and XDSGUI.
June 20, 2024 at 9:36 PM
Technical Updates: Our May software push includesd updates to 21 titles including bedtools, cryosparc-tools, cryoDRGN, deepTools, DIALS, EMReady, IMP, IMOD, Jalview, IGV, MemBrain-Seg, MGLTools, PEET, Phenix, POKY, PyMOL, R, RStudio, Relion, Rosetta, and XDSGUI.
August's software push includes updates to over 20 titles including ACPyPE, AlphaPulldown, Boltz, CCP-EM, ChimeraX, CryoDRGN, Doppio, fpocket, Geneious, Gnuplot, ISOLDE, IsoNet, MDAnalysis, MemBrain-seg, Napari, NMRFx-Analyst, and many more.
More information here: buff.ly/KhZw2Tb
#SBGrid #Software
More information here: buff.ly/KhZw2Tb
#SBGrid #Software
SBGrid Consortium - Software Updates
The SBGrid Consortium is an innovative global research computing group operated out of Harvard Medical School. SBGrid provides the global structural biology community with support for research…
buff.ly
September 10, 2025 at 4:03 PM
August's software push includes updates to over 20 titles including ACPyPE, AlphaPulldown, Boltz, CCP-EM, ChimeraX, CryoDRGN, Doppio, fpocket, Geneious, Gnuplot, ISOLDE, IsoNet, MDAnalysis, MemBrain-seg, Napari, NMRFx-Analyst, and many more.
More information here: buff.ly/KhZw2Tb
#SBGrid #Software
More information here: buff.ly/KhZw2Tb
#SBGrid #Software
Technical Notes: May's software push includes updates to Boltz-1, CNS, cryoDRGN, MemBrain-Seg, ModelAngelo, PyEM, Relion, Scipion, Topaz, XDS, and Xmipp.
More info here: buff.ly/a0Ah8i3
#SBGridSoftware #StructuralBiology
More info here: buff.ly/a0Ah8i3
#SBGridSoftware #StructuralBiology
SBGrid Consortium - Software Updates
The SBGrid Consortium is an innovative global research computing group operated out of Harvard Medical School. SBGrid provides the global structural biology community with support for research…
buff.ly
June 23, 2025 at 4:06 PM
Technical Notes: May's software push includes updates to Boltz-1, CNS, cryoDRGN, MemBrain-Seg, ModelAngelo, PyEM, Relion, Scipion, Topaz, XDS, and Xmipp.
More info here: buff.ly/a0Ah8i3
#SBGridSoftware #StructuralBiology
More info here: buff.ly/a0Ah8i3
#SBGridSoftware #StructuralBiology
We hope MemSplit will make it easier to curate MemBrain-seg outputs for downstream quantitative analysis of membrane ultrastructure. The code and installation instructions are available here: github.com/jredzovic/Me...
July 16, 2026 at 8:33 PM
We hope MemSplit will make it easier to curate MemBrain-seg outputs for downstream quantitative analysis of membrane ultrastructure. The code and installation instructions are available here: github.com/jredzovic/Me...
If you want to split them up into individual segmentations, to assign different colors, or create masks for further processing, etc., membrain-seg has the flag "--store-connected-components", which assigns each connected volume a unique ID.
February 6, 2025 at 11:02 AM
If you want to split them up into individual segmentations, to assign different colors, or create masks for further processing, etc., membrain-seg has the flag "--store-connected-components", which assigns each connected volume a unique ID.
Absolutely! I'm most proficient with using Dragonfly and I've written a protocol for my general workflow here. I also use Amira and the open source tool Membrain Seg! Feel free to DM me if you have questions! bit.ly/3ZNpxlj
Deep Learning-Based Segmentation of Cryo-Electron Tomograms
Watch this Scientific Journal Video about Deep Learning-Based Segmentation of Cryo-Electron Tomograms at JoVE.com
bit.ly
December 10, 2024 at 1:17 AM
Absolutely! I'm most proficient with using Dragonfly and I've written a protocol for my general workflow here. I also use Amira and the open source tool Membrain Seg! Feel free to DM me if you have questions! bit.ly/3ZNpxlj