Beautiful systematic analysis of membrane thickness inside native cells. This is a great use of both the Chlamy Dataset (bsky.app/profile/cell...) and #MemBrain segmentations (bsky.app/profile/lore...). The open-source workflow is a very helpful resource for #TeamTomo. Thanks and congrats!! 🧪 🔬
The talented @lorenzlamm.bsky.social (joint PhD w/ @tingyingpeng.bsky.social) developed #MemBrain 🤖🧠software to automatically segment the thylakoid membranes and localize all the photosystem II (PSII) complexes embedded within them. Let’s get analyzing!👨💻🤓
Try MemBrain:
bsky.app/profile/lore...
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Thanks Alister! That Feynman catchphrase is certainly words to live by for #TeamTomo. I actually used to intro my talks with it. But the trick is in the full quote-- these "easy" observations rely on making our microscopes (and tools for analysis) more powerful. Thanks for your help with #MemBrain 🤗
Beautiful work! And thanks for using #MemBrain. It seems to have segmented pretty well-- nice to see! 😁
Thanks so much! We ❤️ #MemBrain! It is an awesome tool and a key part of our segmentation workflow. The membranes shown here are quantification-mapped surfaces from Surface Morphometrics, downstream of the MemBrain segmentations. I'm grateful for tools that integrate so well across pipelines!
Congrats!!🥳 Awesome work! …and it also makes me happy to see that #MemBrain is cover-worthy 🥰
What's new in #MemBrain v2? Check out the thread from @lorenzlamm.bsky.social below🧵👇. The software now provides a end-to-end pipeline that segments membranes, finds embedded membrane proteins, and quantifies their organization.
#TeamTomo please try it out👩💻. We eagerly await your feedback! 🧪🧶🧬🌾🦠🔬
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! 🧪🧶🧬🔬
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.
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...
