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

"Volume EM: a quiet revolution takes shape" – a review and commentary by Lucy Collinson et al. 2023 on present and future electron microscopy technology and its application https://www.nature.com/articles/s41592-023-01861-8

#vEM #VolumeEM #ElectronMicroscopy

@cyrilpedia @PLOSBiology

Amusing that the piece includes optical microscopy methods unrelated to neural function, such as STED, PALM, expansion microscopy and CLARITY, but ignores electron microscopy methods key to the current boom in #connectomics. In particular, Denk and Horstmann 2004 for SBEM https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0020329 , Knott et al. 2008 for first application of FIBSEM to neuronal tissue https://www.jneurosci.org/content/28/12/2959 , Schalek et al. 2011 for the ATUM serial section tape-collecting system https://academic.oup.com/mam/article-abstract/17/S2/966/6947317 , Xu et al. 2017 for e-FIBSEM and Graham et al. 2019 for GridTape TEM https://www.biorxiv.org/content/10.1101/657346.abstract

#neuroscience #microscopy #VolumeEM #vEM

Electron Microscopy Specialist - cryo-CLEM team

CLF Octopus

Looking for #EM specialist to work on a new #cryoCLEM team at #CLFOctopus facility. Join us to work on exciting #MultidisciplinaryScience

See the full job description on jobRxiv: https://jobrxiv.org/job/clf-octopus-27778-electron-microscopy-specialist-cryo-clem-team/?feed_id=48061

#ScienceJobs #hiring #research #vEM, #cryoFIB-S...
https://jobrxiv.org/job/clf-octopus-27778-electron-microscopy-specialist-cryo-clem-team/?feed_id=48061

RT @davislaundon
Pleased to announce our Methods in Cell Biology #vEM chapter 'Correlative multiscale microCT-SBF-SEM imaging of resin-embedded tissue' is now out!

Below is an example of our workflow used for multiscale imaging of a sample of horse #placenta

https://authors.elsevier.com/a/1guXq,25QIopEv

New software #CebraEM for segmenting membranes and organelles from volume EM:

"CebraEM: A practical workflow to segment cellular organelles in volume SEM datasets using a transferable CNN-based membrane prediction", by Hennies et al. 2023 https://www.biorxiv.org/content/10.1101/2023.04.06.535829v1.full from Anna Kreshuk's and Yannick Schwab's labs at #EMBL.

#neuroscience #CellBiology #vEM #volumeEM #MachineLearning #ComputerVision

@vuhlmann

"MorphoFeatures for unsupervised exploration of cell types, tissues, and organs in volume electron microscopy"
Valentyna Zinchenko et al. 2023 https://elifesciences.org/articles/80918 with @vuhlmann Arendt & Kreshuk labs

"We further illustrate how our features can facilitate the detection of cell types by morphological means, via similarity-based clustering in the MorphoFeature vector space, sorting the cells into morphologically meaningful groups that show high correlation with genetically defined types such as muscle cells and neurons."

#neuroscience #ElectronMicroscopy #vEM #Platynereis

RT @notjustmoore
"Toward #scalable reuse of #vEM data: #OMEZarr to the rescue" just hit the shelves!📚

https://doi.org/10.1016/bs.mcb.2023.01.016

Special thanks to co-authors @normanrz & @BogovicJohn, co-artist @DrHenningFalk, and volume (ha!) editors @EM_STP @KedarNarayan2 & @PaulVerkade

👏👏👏#VolumeEM @VolumeEM1
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RT @notjustmoore
"Toward #scalable reuse of #vEM data: #OMEZarr to the rescue" just hit the shelves!📚

https://doi.org/10.1016/bs.mcb.2023.01.016

Special thanks to co-authors @normanrz & @BogovicJohn, co-artist @DrHenningFalk, and volume (ha!) editors @EM_STP @KedarNarayan2 & @PaulVerkade
https://twitter.com/notjustmoore/status/1633865042025127937

"Toward #scalable reuse of #vEM data: #OMEZarr to the rescue" just hit the shelves!📚

https://doi.org/10.1016/bs.mcb.2023.01.016

Special thanks to co-authors @normanrz & @BogovicJohn@twitter.com, co-artist @DrHenningFalk@twitter.com, and volume (ha!) editors Lucy Collinson, Kedar Narayan, & Paul Verkade

Not to mention @ome + @zarr

This is awesome! A great proof of principle as well as I have not seen any other example of automated segmentation of so many classes from a cryoFIBSEM dataset. Congrats! If you would publish a protocol and/or the UNet, I think there would be a lot of people in #vEM interested.
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RT @parameciumbrain
This was a fun challenge! empiar 11275, A full chlamydomonas cell. Looks so cool in 3D! I used a pre-trained UNet from @OrsDragonfly…
https://twitter.com/parameciumbrain/status/1624978507364171780

@vigji @jason_ritt @csdashm @NicoleCRust @neurobongo @xaq

The midbrain-hindbrain in a mouse is presently too big for #connectomics with #vEM #volumeEM.

Instead, try a small frog or lizard. That's what we aim for.

@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

Curious how #Lichen look on the inside?

Here a (not very sophisticated) volume imaging of Xanthoria parietina. Who can help to identify the different cell types/species?

#LichenSubscribe #PlantScience #Multicellularity #FIBSEM #VolumeImaging #vEM

@BWJones Welcome Brian to #neuroscience! It’s customary to make an introductory posts with hashtag # introduction (I’m adding a space to spoof it). Also, hashtags are the gateway to finding people and posts, and you can follow hashtags just like you follow people. You may be interested in #connectome #connectomics #vEM #volumeEM #photography given your contributions to these fields :-)

@patrickmineault @neuralreckoning @ShahabBakht

There’s early work from Srini Turaga’s lab on a simulation of the #Drosophila optic lobes, for the #vEM reconstructed #connectome from photoreceptors to the direction-selective neurons:

Tschopp FD, Reiser MB, Turaga SC. A connectome based hexagonal lattice convolutional network model of the Drosophila visual system. arXiv preprint arXiv:1806.04793. 2018 https://arxiv.org/abs/1806.04793
#neuroscience

Quite pleased with our preprint on the connectome of the whole #Drosophila larval brain, as reconstructed with #CATMAID from #vEM #volumeEM and analysed from a graph-theoretic perspective.

The bioRxiv lists ~10,000 abstract views and nearly ~2,000 PDF downloads over two weeks. Thanks so much everyone for your interest in our research!

Preprint: https://www.biorxiv.org/content/10.1101/2022.11.28.516756v1

See original #tootorial thread:
https://mathstodon.xyz/@albertcardona/109422190525090990

@NicoleCRust @complexsystems @cogneurophys @PessoaBrain @SussilloDavid @carlosbrody @Neurograce @neuralreckoning @tyrell_turing @DrYohanJohn @cian @WiringtheBrain @tdverstynen @neuralengine

I find Kim & Bassett 2022 "A Neural Programming Language for the Reservoir Computer" https://arxiv.org/abs/2203.05032 rather promising. In part because #vEM #connectomics is showing brains are both modular and recursive as hell, which fits well.
#neuroscience

#introduction http://mstdn.science

I am a #cryoFIB, #PFIB, #vEM and #devbio enthusiast at MPI Biochemistry pushing #TeamTomo #tech for higher throughput by developing software #SerialFIB (#OpenSoftwareAcceleratesScience) and wider variety of samples by HPF, cryo-lift-out …

3,013 neurons, half a million synapses: the complete #connectome of the whole #Drosophila larval brain!

Winding, Pedigo et al. 2022. "The connectome of an insect brain" https://www.biorxiv.org/content/10.1101/2022.11.28.516756v1

We’ve mapped and analysed its circuit architecture, from sensory neurons to brain output neurons, as reconstructed from volume electron microscopy, and here is what we found. 1/

#neuroscience #connectomics #vEM #volumeEM