Mastodawn

If your server uses the django framework, beware of SIGPIPE calls:
https://github.com/catmaid/CATMAID/commit/1de3b8c0a4a1623cf24c047e28c1bd247dd42ef8

In #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.

#python #django

Doc: add info about rogue uWSGI processes on SIGPIPE · catmaid/CATMAID@1de3b8c

This one was rather hard to track down. Some more details can be found here: https://github.com/unbit/uwsgi/issues/1786

GitHub

Albert Cardona Nov 4

"Just use Postgres until it breaks."
https://topicpartition.io/blog/postgres-pubsub-queue-benchmarks

We 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."

Kafka is fast -- I'll use Postgres

Why you should just use Postgres instead of Kafka for small-scale message queuing and pub-sub patterns. Benchmarks and practical tests included.

TopicPartition

dancwart Jul 3, 2025

Happy Pancake Thursday!

I'm busy preparing for a trip, so I've had very little time for art lately. But that's no excuse to not honour the tradition.

Drawn in paint using a mouse

#pancakethursday #pancakes #cat #kemonomimi #catmaid #microsoftpaint #art #MastoArt

Albert Cardona Apr 2, 2025

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

#neuroscience #CATMAID

CATMAID

Miku Mar 18, 2025

Today maid is very proud to present you my masters castle 😊😊🩷🩷 #uwu #fyu #cosplay #kawaiigirl #maids #catmaid

dancwart Dec 26, 2024

Merry Pancakemas, and happy last Pancake Thursday of the year!

#christmas #christmas2024 #pancakethursday #pancakes #cat #kemonomimi #catmaid #maid #originalcharacter #art #MastoArt

Show thread

Teixi Oct 11, 2024

@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!

Show thread

Albert Cardona Sep 13, 2024

@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

#neuroscience #connectomics