#volumeem — Public Fediverse posts

@innuendo @jernej__s @ZachWeinersmith

Our eFIB-SEM (as per Xu et al. 2017 https://elifesciences.org/articles/25916 ) runs 24/7 for up to 8 weeks, when it runs out of source. And it's essential that it does so, uninterrupted, since it's imaging at nanometre resolution, milling 2 nm slices at a time with an ion beam and then repeatedly imaging the block face. The process is unsurprisingly very sensitive; was hard enough to overcome the reheat cycle of the instrument itself (every 60 hours or so) by detecting it, de-engaging the beams and then seamlessly re-engaging with the block face.

A brief video of the kind of data we acquire:
https://youtu.be/p4MH4-I-P5I

The MS Windows computer deciding to reboot on its own is unacceptable.

#ElectronMicroscopy #Zeiss #FIBSEM #VolumeEM #vEM #Drosophila

"SmartEM: machine learning-guided electron microscopy", by Meirovitch et al. 2025 (Shavit's, Samuel's and Lichtmann's lab).

https://www.nature.com/articles/s41592-025-02929-3

#neuroscience #VolumeEM #SmartEM #ElectronMicroscopy #vEM

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

#volumeEM #ElectronMicroscopy #CLEM

"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.

#neuroscience #Drosophila #connectomics #vEM #volumeEM

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

@nanographs

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.

https://www.biorxiv.org/content/10.1101/657346v1

#vEM #volumeEM #TEM

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

#FijiSc #java #jython #volumeEM #vEM

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."

https://www.nature.com/articles/s41592-024-02227-4.epdf?sharing_token=nElv1SiMTpxjPsXqxX9xMtRgN0jAjWel9jnR3ZoTv0Nrov_SWdBALYS97F1eM5Lk_JEBGPmcigRE4GeE5PJKr0YlUmXLIqorYFzRm9BanPX-UNoWn8B-lFTNgSYQl_gdPFu85a_vT5pFp1FCyd6dRPVpDqcS14IBc1pS4_ue4ho%3D

#connectomics #volumeEM #vEM #neuroscience #MaxPlanckSociety

“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

#neuroscience #vEM #VolumeEM

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

Job ad:
https://career5.successfactors.eu/career?career%5fns=job%5flisting&company=universitdP&navBarLevel=JOB%5fSEARCH&rcm%5fsite%5flocale=fr%5fFR&career_job_req_id=21524&selected_lang=fr_FR&jobAlertController_jobAlertId=&jobAlertController_jobAlertName=&browserTimeZone=Europe/Zurich&_s.crb=bYQhIgqn0MbzwdRaA%2baluxpeS0wy0UARIy5GFiKiaEU%3d

#FediHire #ElectronMicroscopy #CryoEM #vEM #VolumeEM

A connectome of the optic lobe of the extremely tiny fairy wasp, Megaphragma sp.

"A complete reconstruction of the early visual system of an adult insect", by Chua et al. 2023 (Chklovskii & Polilov) https://www.sciencedirect.com/science/article/pii/S096098222301237X

Don't miss the supplemental figures.

"Compared with the honeybee and the fruit fly, Megaphragma exhibits the following miniaturization-related adaptations: a significant reduction in the number of ommatidia, absence of several cell types, reduced size, and denucleation of neurons. Interestingly, the reduction in lens diameter is less than that expected from the optimization of the optical resolution of the eye. This suggests that light sensitivity is a more important
consideration when lens diameter approaches the wavelength of light. The absence of wide-field (or non-columnar) lamina neurons in Megaphragma could be a consequence of the smaller number of ommatidia, their larger acceptance angle, and the lower resolving power of the eye."

Volume assembled with #FijiSc and #TrakEM2, and its neurons and synapses mapped with #CATMAID. Woohoo!

#neuroscience #connectomics #VolumeEM #vEM #insects #miniaturization

Following from Collinson's paper, here is my take on scaling up volume electron microscopy for connectomics in the #UK or any country willing to commit about 10 to 20 million a year:

"Growing and nurturing a research base in connectomics"
https://albert.rierol.net/tell/20230823_connectomics_research_base.html

From the humble #Drosophila to the #mouse brain, passing through the mosquito, honeybee, gecko lizards and the Etruscan shrew.

It's possible, it's feasible, it's timely: therefore we must.

#neuroscience #connectomics #VolumeEM #vEM

@remenca @spla @marcbeldata

Doncs ...

#BigStitcher https://www.nature.com/articles/s41592-019-0501-0

#BigDataViewer https://www.nature.com/articles/nmeth.3392

#ImgLib2 https://academic.oup.com/bioinformatics/article-abstract/28/22/3009/240540

#CATMAID https://academic.oup.com/bioinformatics/article-abstract/25/15/1984/210794

Elastic volume registration https://www.nature.com/articles/nmeth.2072

#vEM #volumeEM https://l1em.catmaid.virtualflybrain.org/?pid=1&zp=59900&yp=36430.399999999994&xp=32311.00000000001&tool=tracingtool&sid0=1&s0=3

@remenca @spla @marcbeldata

Doncs ...

#BigStitcher https://www.nature.com/articles/s41592-019-0501-0

#BigDataViewer https://www.nature.com/articles/nmeth.3392

#ImgLib2 https://academic.oup.com/bioinformatics/article-abstract/28/22/3009/240540

#CATMAID https://academic.oup.com/bioinformatics/article-abstract/25/15/1984/210794

Elastic volume registration https://www.nature.com/articles/nmeth.2072

#vEM #volumeEM https://l1em.catmaid.virtualflybrain.org/?pid=1&zp=59900&yp=36430.399999999994&xp=32311.00000000001&tool=tracingtool&sid0=1&s0=3

@remenca @spla @marcbeldata

Doncs ...

#BigStitcher https://www.nature.com/articles/s41592-019-0501-0

#BigDataViewer https://www.nature.com/articles/nmeth.3392

#ImgLib2 https://academic.oup.com/bioinformatics/article-abstract/28/22/3009/240540

#CATMAID https://academic.oup.com/bioinformatics/article-abstract/25/15/1984/210794

Elastic volume registration https://www.nature.com/articles/nmeth.2072

#vEM #volumeEM https://l1em.catmaid.virtualflybrain.org/?pid=1&zp=59900&yp=36430.399999999994&xp=32311.00000000001&tool=tracingtool&sid0=1&s0=3

@remenca @spla @marcbeldata

Doncs ...

#BigStitcher https://www.nature.com/articles/s41592-019-0501-0

#BigDataViewer https://www.nature.com/articles/nmeth.3392

#ImgLib2 https://academic.oup.com/bioinformatics/article-abstract/28/22/3009/240540

#CATMAID https://academic.oup.com/bioinformatics/article-abstract/25/15/1984/210794

Elastic volume registration https://www.nature.com/articles/nmeth.2072

#vEM #volumeEM https://l1em.catmaid.virtualflybrain.org/?pid=1&zp=59900&yp=36430.399999999994&xp=32311.00000000001&tool=tracingtool&sid0=1&s0=3