@uni_matrix @davi

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!

@CurrentBiology

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-1

See 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

@Raf

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/

@adredish @neuralreckoning @brembs @ScholarNexus

Likewise for #TrakEM2, #FijiSc and #catmaid software – except we did write papers for them.

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

@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 :)

@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.

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!

#neuroscience #connectomics
/END

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)

#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/

@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.