"SmartEM: machine learning-guided electron microscopy", by Meirovitch et al. 2025 (Shavit's, Samuel's and Lichtmann's lab).
#volumeEM
Zurich Winter School 2026 on electron microscopy techniques, run by Dr. Miriam Lucas and colleagues.
Dates: January 19-23rd, 2026
Apply by November 17th, 2025.
"A hands-on, week-long course for PhD students, postdocs, and microscopy enthusiasts eager to deepen their expertise in cutting-edge microscopy techniques."
🎯 Practical modules on Advanced and Super-Resolution LM, Sample Preparation for EM, CLEM, and volume EM
https://scopem.ethz.ch/education/schools/WinterSchool2026.html
Ctenophores possess a unique aboral organ that acts as a multisensory center, controlling complex behaviors. We’ve now created a ctenophore model integrated with our 3D volume EM data. Puts it into perspective. Check out our recent work here: www.biorxiv.org/content/10.1... #ctenophores #volumeEM
From Elizabeth Marin at Zoology Dept., Cambridge University:
"Together with Greg Jefferis (MRC LMB, Cambridge), Wei-Chung Allen Lee (Harvard Medical School), and Meg Younger (Boston University), I have secured a £4.8M Wellcome Discovery Award to generate a mosquito brain connectome and investigate chemosensory circuits involved in human host-seeking."
"We are currently recruiting for two research assistant positions based in the Zoology department at Cambridge University. Please share this post with any likely candidates :)."
"Comparative connectomics of Drosophila descending and ascending neurons", Tomke Stürner et al. 2025 (Greg Jefferis and Katharina Eichler's labs).
https://www.nature.com/articles/s41586-025-08925-z
Compares between males and females.
We had our very first practical school at the Centre for Organismal Studies at @uniheidelberg !
This was a hands-on volume EM and sample preparation course with several theoretical lectures.
https://www.cos.uni-heidelberg.de/en/research-groups/gaspar-jekely/Events/zoocell-course
Here is a short write up about the event by @abilgk
https://zoocell.eu/2025/03/13/practical-course-on-animal-diversity-and-em-sample-preparation/
🚀 Starting in a few hours! Join leading experts as they share insights on handling large #VolumeEM datasets & improving collaborative workflows.
📅 March 6 | 5-7PM CET | Online | Free
🔗 Register now: https://buff.ly/LaZw4aA.
More #introduction about our ZooCELL network.
We will do a lot of volume electron #microscopy #volumeEM focusing on sensory systems in marine #animals
We will combine this with single-cell #genomics, correlative LM/EM, #AI -based image segmentation and classification, and genetics
You can read more about the participating labs here:
https://zoocell.eu/consortium/#Beneficiaries
We will post about events, projects etc. in the coming years.
If you like #zoology #evodevo #marine #biology follow/boost us!
⏳ 4 more days to go! Don't miss our online symposium on #VolumeEM data challenges - practical solutions for massive datasets & collaboration.
📅 March 6, 2025 | 5-7PM CET | Free registration
🔗 Sign up: https://buff.ly/LaZw4aA.
Join our online symposium on #VolumeEM data challenges! Experts will share practical solutions for handling massive datasets & improving collaboration.
📅 March 6, 2025 | 5-7PM CET | Online | Free registration
Sign up for free at https://buff.ly/42gkyv4.
Join us for the last Pub before the Winter Break! ☃️
We'll learn about #VolumeEM approaches from the experts at #EuroBioImaging’s Advanced Light & Electron Prague Node, part of the Volume EM community.
🗓️Fri, Dec 20 @ 13:00 CET
All are welcome 🔽
https://www.eurobioimaging.eu/events/diverse-vem-techniques-and-applications-at-the-laboratory-for-electron-microscopy-ceskebudejovice/
On my way to #vEMTechForum2024. Looking forward to talking about large vEM data and other fun challenges! #volumeEM @webknossos
GridTape TEM with beam deflection to reduce stage movements and increase imaging throughput:
"Fast imaging of millimeter-scale areas with beam deflection transmission electron microscopy", Zhao et al. 2024
https://www.nature.com/articles/s41467-024-50846-4
#TEM #GridTapeTEM #vEM #VolumeEM #connectomics #neuroscience #microscopy #ElectronMicroscopy
Thanks for sharing this – will have to think about it. In our case, we built in-house the gridtape reel holders which amount to a custom stage with a mini-camera in it for identifying slots and controlling imaging. So we don't use the factory-supplied stage.
True as always that the way to make software run faster is to make it do less operations. After all, CPUs can only execute a fixed number of operations per unit of time.
Here, I tweaked code for serial section registration that drops execution time from 27 seconds to 100 milliseconds: a 270x speed up.
All it had to do is to search for matching SIFT features in one image only within a predetermined radius centered on one SIFT feature in another image. Extremely effective for when e.g., the maximum translation is known.
The matching code using a KDTree:
https://github.com/acardona/scripts/blob/master/java/asm/my/PointMatchesFast.java#L56
The test script:
https://github.com/acardona/scripts/blob/dev/python/imagej/FIBSEM/tests/test_matchNearbyFeatures.py
From Moritz Helmstaedter on #RoboEM:
"In today’s AI research, any project lasting longer than 6 months is considered slow, if not outdated and overrun by history. RoboEM, with a concept and an approach that seem quite plausible, still took 5 years from idea to the fully evaluated tool reported here. This was only possible with the patient support of the Max Planck Society, which encourages long-term projects, and the tenacity of the first author. Details made all the difference. And, as often, dead ends had to be avoided efficiently. We had to abandon, for example, the idea of using steering variability to indicate branch points — a nice analogy to road intersections in car steering, but too far-fetched to work well enough in brain tissue data. Sometimes giving up beloved ideas is as important as following through on others. M.H."
#connectomics #volumeEM #vEM #neuroscience #MaxPlanckSociety
We have now published a new and massively extended/reworked preprint of the whole-body #Platynereis larval #connectome with over 50 figures
https://www.biorxiv.org/content/10.1101/2024.03.17.585258v1
All the analyses, plots and figures should be reproducible in #rstats with the code provided:
https://zenodo.org/doi/10.5281/zenodo.10825370
by querying our public #CATMAID database:
“Perception: How larvae feel the world around them” by Jimena Berni https://elifesciences.org/articles/96708
… an insight piece on Andreas Thum’s lab work on mapping the sensory organs of the #Drosophila larva with electron microscopy:
“Morphology and ultrastructure of external sense organs of Drosophila larvae”
Richter et al. 2024 https://elifesciences.org/articles/96708
Christel Genoud is recruiting an electron microscopy specialist at the University of Lausanne:
https://wp.unil.ch/emf/?trk=feed-detail_main-feed-card-text
EM stack of a golgi ribbon in a glial cell of #Platynereis, from Benvenuto et al.,:
"Evolution of the ribbon-like organization of the Golgi apparatus"
with small contribution from our lab.
https://www.sciencedirect.com/science/article/pii/S2211124724001190?via%3Dihub
#CellBiology #volumeEM #cell
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