#catmaid — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #catmaid, aggregated by home.social.
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If your server uses the django framework, beware of SIGPIPE calls:
https://github.com/catmaid/CATMAID/commit/1de3b8c0a4a1623cf24c047e28c1bd247dd42ef8In #catmaid we were seeing lots of uwsgi processes going rogue, turns out they were stuck in a loop. Tom Kazimiers successfully figured this out and found a configuration to avoid the issue.
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"Just use Postgres until it breaks."
https://topicpartition.io/blog/postgres-pubsub-queue-benchmarksWe are far from that – we use #postgres to power #CATMAID for #connectomics and so far so good.
"Donald Knuth warned us in 1974 - premature optimization is the root of all evil. ... The point of this article is to show you that this “small scale” number has grown further than what people remember it to be - it can comfortably mean many megabytes per second. We are in a Postgres Renaissance for a reason: Postgres is frequently good enough. Modern NVMEs and cheap RAM allow it to scale absurdly high."
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Sometimes one stops to just look at the data. And the software user interface. They are beautiful.
We are looking at a cross section of the #Drosophila larval brain, near the brain commissure, where hundreds of neurons (magenta: their reconstructed skeletons) cross from one brain hemisphere to the other. To the right, a 3D rendering of multiple neurons, a pair of which cross the midline in a U-shaped bend.
Our CATMAID software is web-based, in other words it's just a website that accesses remote data. I credit it's sleek design to @herrsaalfeld – author of the early, "Ice Age" CATMAID and its blue tones – who at some point in his life studied "medieninformatik" and has always had a penchant for art.
See our images and fly neurons here, kindly hosted by the #VirtualFlyBrain :
https://l1em.catmaid.virtualflybrain.org/?pid=1&zp=33100&yp=31179&xp=53333&tool=tracingtool&sid0=1&s0=2 -
Merry Pancakemas, and happy last Pancake Thursday of the year!
#christmas #christmas2024 #pancakethursday #pancakes #cat #kemonomimi #catmaid #maid #originalcharacter #art #MastoArt
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ps: also includes nice paragraph on #TrakEM2 by @albertcardona et al. w/ remark on alignments errors auto correction.
As for #catmaid collaborative annotation & neuronal structures skeletons approach!
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Andreas Schoofs and Anton Miroschnikow in Michael Pankratz' lab have done an astonishing amount of work manually mapping the peripheral nervous system of the larval #Drosophila, with #CATMAID, in the STEM volume we imaged and they named "Igor". Congrats on seeing this gargantuan project through!
The whole larval volume of "Igor", including all tissues, is available here, courtesy of the #OpenOrganelle project led by Aubrey Weigel @avweigel at #HHMIJanelia:
https://openorganelle.janelia.org/datasets/jrc_fly-larva-1See it at 5x5x35 nm resolution in #neuroglancer: https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22:%7B%22x%22:%5B1e-9%2C%22m%22%5D%2C%22y%22:%5B1e-9%2C%22m%22%5D%2C%22z%22:%5B1e-9%2C%22m%22%5D%7D%2C%22position%22:%5B249600.5%2C79040.5%2C84280.5%5D%2C%22crossSectionOrientation%22:%5B0%2C1%2C0%2C0%5D%2C%22crossSectionScale%22:50%2C%22projectionOrientation%22:%5B0%2C1%2C0%2C0%5D%2C%22projectionScale%22:65536%2C%22layers%22:%5B%7B%22type%22:%22image%22%2C%22source%22:%22n5://s3://janelia-cosem-datasets/jrc_fly-larva-1/jrc_fly-larva-1.n5/em/tem-uint8%22%2C%22tab%22:%22rendering%22%2C%22opacity%22:1%2C%22blend%22:%22additive%22%2C%22shader%22:%22#uicontrol%20invlerp%20normalized%28range=%5B0%2C%20255%5D%2C%20window=%5B0%2C%20255%5D%29%5Cn#uicontrol%20vec3%20color%20color%28default=%5C%22white%5C%22%29%5Cnvoid%20main%28%29%7BemitRGB%28color%20%2A%20normalized%28%29%29%3B%7D%22%2C%22name%22:%22tem-uint8%22%7D%5D%2C%22selectedLayer%22:%7B%22visible%22:true%2C%22layer%22:%22tem-uint8%22%7D%2C%22crossSectionBackgroundColor%22:%22#000000%22%2C%22layout%22:%224panel%22%7D (control-minus and control-plus to zoom; mouse click to pan, scroll wheel to browse in Z).
Will appear at the #VirtualFlyBrain website soon as well.
There are many more peripheral nervous system components mapped, yet to be published.
This paper is open access:
"Serotonergic modulation of swallowing in a complete fly vagus nerve connectome", Schoofs et al. 2024 https://www.cell.com/current-biology/fulltext/S0960-9822(24)01137-0?rss=yes&utm_source=dlvr.it&utm_medium=mastodon -
"May I take your order, dear customer... I highly recommend the pancakes"
#jojosbizarreadventure #jba #parody #OriginalCharacter #catmaid #art #MastoArt
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El PostGIS funciona de meravella. Fa anys i panys que el fem servir per a la base de dades de #CATMAID, el nostre programari lliure per a mapar neurones en volums de sistemes nerviosos:
https://catmaid.readthedocs.io/ -
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:
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@adredish @neuralreckoning @brembs @ScholarNexus
Likewise for #TrakEM2, #FijiSc and #catmaid software – except we did write papers for them.
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Some #fursuit pics from #onicon this past weekend!
Should I post more? 👀
#Furry #furryart #fursuiter #onicon2023 #catmaid #maid #legs #paws #photography #handmade #cat #kitty #calico #fursuitfriday
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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
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Avui ha sortit publicada la versió avaluada per experts del nostre article descrivint el #connectoma [1] del cervell de la larva de la mosca del vinagre. Unes 3,000 neurones i més de mig milió de sinàpsis, traçades a mà amb el nostre programmari especialitzat i de codi obert, #Catmaid. En anglès, aquí:
"The connectome of an insect brain"
https://www.science.org/doi/10.1126/science.add9330#Vilaweb se n'ha fet ressò: https://www.vilaweb.cat/noticies/cervell-neurona-neurona-investigacio-deu-anys-crea-mapa-mes-complex-mai-fet/
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Today the peer-reviewed version of our preprint is out:
"The #connectome of an insect brain"
https://www.science.org/doi/10.1126/science.add9330Congrats to co-first authors Michael Winding and Benjamin Pedigo, and to all our lab members and collaborators who made this work possible over the years. A journey that started over 10 years ago–and yet this is but a new beginning. So much more to come.
See my #tootprint on the preprint from back in the Autumn: https://mathstodon.xyz/@albertcardona/109422190525090990
The data is available both as supplements and directly via #CATMAID thanks to hosting by the #VirtualFlyBrain:
https://l1em.catmaid.virtualflybrain.org/?pid=1&zp=108250&yp=82961.59999999999&xp=54210.799999999996&tool=tracingtool&sid0=1&s0=2.4999999999999996&help=true&layout=h(XY,%20%7B%20type:%20%22neuron-search%22,%20id:%20%22neuron-search-1%22,%20options:%20%7B%22annotation-name%22:%20%22papers%22%7D%7D,%200.6)(The "Winding, Pedigo et al. 2023" annotation listing all included neurons will appear very soon in an upcoming update.)
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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
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In this paper we generated most of the figures entirely in R for open science and reproducibility. All code is shared here:
https://github.com/JekelyLab/Jasek_et_al
The figures and analyses can be regenerated by the code that will query our public #CATMAID database where all EM data, tracings and annotations are shared:
https://catmaid.jekelylab.ex.ac.uk (project id: 11)
#openscience #rstat -
@dantracey @kristinmbranson @annikabarber @debivort @giorgiogilestro
Find the original basin-1 neurons at the #VirtualFlyBrain at "Tools - CATMAID - Hosted EM Data - Larval - Larva (ABD1.5)" which opens a #CATMAID server https://abd1.5.catmaid.virtualflybrain.org/?pid=1&zp=10485&yp=40560.65722061269&xp=42396.0789533435&tool=tracingtool&sid0=1&s0=4.5&help=true&layout=h(XY,%20%7B%20type:%20%22neuron-search%22,%20id:%20%22neuron-search-1%22,%20options:%20%7B%22annotation-name%22:%20%22papers%22%7D%7D,%200.6)
Find them via Neuron Search (icon with a "?").
The "Construction time" is wrong (see "Summary info" of the Selection Table) because these neurons were imported from #TrakEM2. Old enough to predate the #CATMAID software!
#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 -
@Gontijo Thanks! And very good question: I'm preparing a guide everyone on finding their favourite #Drosophila larval neurons in #CATMAID.
1st, all neurons will appear in the VirtualFlyBrain website soonish. We have to send in an update with all neurons newly added in this paper.
2nd, there are tools from @drosofriend's and Douglas Armstrong's lab for NBLASTing James W. Truman catalogue of LSM images of GAL4 lines (GMR and Vienna tiles) against EM-reconstructed neurons.
All in due time :)
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El cervell d'una mosca. O més ben dit: el cervell de la larva d'una mosca.
3013 neurones i mig milió de sinapsis. Reconstruïdes a mà, gràcies al software lliure #CATMAID i l'esforç de més de 80 persones al llarg de 10 anys. Tota una fita, si ho puc dir jo mateix, que en sóc una d'aquestes 80 i he ensenyat a totes les altres com fer-ho tot això.
L'article d'accés lliure, aquí: https://www.biorxiv.org/content/10.1101/2022.11.28.516756v1
Fil en anglès repassant-ne les troballes: https://mathstodon.xyz/@albertcardona/109422190525090990
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@mhl20 Thanks Marc! #CATMAID lists ~8,000 hours of reconstruction work and ~3,000 hours of proofreading work to complete the whole #Drosophila larval brain #connectome. And as you know this is likely an underestimate.
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A huge THANK YOU to everyone that worked on this project for 10 years, starting with first co-authors Michael Winding and Ben Pedigo at University of Cambridge and Johns Hopkins. A collaboration with Marta Zlatic, Carey E. Priebe, and Joshua Vogelstein.
This work started at #HHMIJanelia and continued at the #MRCLMB in Cambridge, UK.
All neuron reconstructions were done painstakingly by hand with #CATMAID by over >80 people! Thanks so much!
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The web-based open source software #CATMAID was devised as "google maps but for volumes". Documentation at https://catmaid.org and source code at https://github.com/catmaid/CATMAID/
Modern #CATMAID enables hundreds of #neuroscience researchers world wide to collaboratively map neuronal circuits in large datasets limited only by bandwidth and server-side storage to map and analyse a whole brain #connectome.
See the #Drosophila larval CNS at the #VirtualFlyBrain server: https://l1em.catmaid.virtualflybrain.org/?pid=1&zp=108250&yp=82961.59999999999&xp=54210.799999999996&tool=tracingtool&sid0=1&s0=2.4999999999999996&help=true&layout=h(XY,%20%7B%20type:%20%22neuron-search%22,%20id:%20%22neuron-search-1%22,%20options:%20%7B%22annotation-name%22:%20%22papers%22%7D%7D,%200.6)
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#TrakEM2 runs as a plugin of #FijiSc https://fiji.sc/ and in fact motivated the creation of the #FijiSc software in the first place, to manage its many dependencies and facilitate distribution to the broader #neuroscience community.
#TrakEM2 was founded in 2005, when TB-sized datasets were rare and considered large. Largest dataset I've successfully managed with #TrakEM2 was ~16 TB. For larger volumes see #CATMAID.
For 3D visualization #TrakEM2 uses the 3D Viewer https://imagej.net/plugins/3d-viewer/
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@manlius Yes, a lot, but generated mostly with #CATMAID which is more purpose-built for #connectomics.
An early reconstruction of a neural circuit done with #TrakEM2 was by Davi Bock et al. 2011 on the mouse visual cortex, "Network anatomy and in vivo physiology of visual cortical neurons" https://www.nature.com/articles/nature09802
Another one with #TrakEM2 was by Dan Bumbarger et al. 2013 "System-wide rewiring underlies behavioral differences in predatory and bacterial-feeding nematodes" where they compared #celegans with another nematode, #pristionchus pacificus that has the exact same amount of neurons but connected differently https://www.sciencedirect.com/science/article/pii/S0092867412015000
Later ones with #CATMAID include:
The polychaete worm #Platynereis by @jekely 's group, "Whole-animal #connectome and cell-type complement of the three-segmented Platynereis dumerilii larva" Verazto et al. 2020 https://www.biorxiv.org/content/10.1101/2020.08.21.260984v2.abstract
And all of ours in #Drosophila larva. See the #VirtualFlyBrain server which hosts the #vEM of the whole central nervous system and lists all the neurons included in each published paper (currently 23), shared among the papers and all connecting to each other: https://l1em.catmaid.virtualflybrain.org/?pid=1&zp=108250&yp=82961.59999999999&xp=54210.799999999996&tool=tracingtool&sid0=1&s0=2.4999999999999996&help=true&layout=h(XY,%20%7B%20type:%20%22neuron-search%22,%20id:%20%22neuron-search-1%22,%20options:%20%7B%22annotation-name%22:%20%22papers%22%7D%7D,%200.6)
The 24th will come soon, featuring the complete whole #Drosophila larval brain with ~2,500 neurons. It's under review.
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@spla @marcos Hom es pregunta quan trigarà a sortir una implementació del protocol d'ActivityPub en #rust o #cpp o #java o quelcom semblant.
Ara que això que dius que el crear comptes triga molt em sona a una situació de performance tuning de la base de dades. És #postgresql oi? La fem servir per a #CATMAID i alguns settings tenen un impacte desmesurat en la performance.