Seth Tomchik @sethtomchik@qoto.org

I spent some time working on making a setup to image muscle activity in walking flies. The leg moves out of the field of the view often, so we set up a light field microscope. It's just like a normal microscope, but with a microlens array filter added so the image comes out with a bunch of tiny lenslets. You can use to reconstruct a full volume from a single image!

We found the light field framework oLaF to work really well in reconstructing the volume (as you can see on the right image). It would take 20 minutes per image though, which would take too long for processing whole videos.

So I've made pyolaf! https://github.com/lambdaloop/pyolaf

It's a port of oLaF from Matlab to Python, with some optimizations to make it use the GPU effectively. With this, it can run at least 20x faster!

#neuroscience #microscopy #imaging

@biorxivpreprint Elias Scheer’s thesis work is up on bioRxiv! It uncovers links between different foraging behaviors, including a classical ethological decision, abandoning a patch of food.

The full connectome of the fruit fly is slowly being mapped out.
But how do we make sense of it? Sometimes the anatomy is highly suggestive of a function, but more often than not there are much more connections than we expect and the interpretation is complicated.

I've been slowly collecting papers that try to link a simulation of the connectome with a fly behavior.

Here, I'd like to share one such paper, which uses modeling and connectomics to study the link between development and fly preferences for a particular odor.

The paper is:
"Neural correlates of individual odor preference in Drosophila"
Churgin & Lavrentovich et al
(senior author @debivort )
https://www.biorxiv.org/content/10.1101/2021.12.24.474127v1

I presented the paper in the @tuthill journal club this week and wanted to share it here while it's still in my head! 🧵

#modeling #connectomics #Drosophila #neuroscience #PaperThread #JournalClub

Every time someone says they did a GWAS for a complex trait, my eyes roll so hard you can *hear* them. But every now and again, people do serious validation! A PA-TX collab finds GPI anchor biosynthesis as a regulator of sleep in flies and fish. https://doi.org/10.1126/sciadv.abq0844

Silent snow. Location Kyoto. #followfriday #streetphotography #photography

PHOTO BLOG: Earlier this month, a storm chaser from the Netherlands took a wonderful photo showing several textbook ice halos, including a 46-degree halo, a 22-degree halo with parhelion (sun dogs), and an upper tangent arc. https://www.accuweather.com/en/leisure-recreation/live-news/weather-permitting-photo-blog/933860

135 years ago, James Blyth dreamed of a future in which every house would be lit by a wind turbine, and argued that wind power was good for the environment and cheaper than fossil fuels.

Blyth was ahead of his time but, unfortunately, not on the money:

https://www.theguardian.com/environment/2022/dec/22/james-blyth-scottish-engineer-wind-power

#JamesBlyth #ClimateCrisis #RenewableEnergy #WindPower #renewables #wind

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

Atlantic Puffins float on the ocean near Machias Seal Island. International Waters between Maine and Canada, summer 2022

I wrote a piece for the New York Times about how scientists used Twitter during the Covid pandemic and about what comes next.

https://www.nytimes.com/2022/11/19/opinion/pandemic-twitter.html?smid=nytcore-ios-share&referringSource=articleShare

An Incredible Day In Internet History

It started with the Twitter lockout. 10,000 new users per hour. A QUARTER MILLION people migrated to Mastodon in one day. The servers struggled. Remarkably, admins all over the world built up capacity in real time. New users were patient. The system held.

It's running better now. There will be more hard days ahead, but people powered social media has arrived.

#twittermigration #NewUsers #Welcome

Happy FlyDay everyone! (11/18)

#Drosophila

My very first "tootorial", we have a new preprint out, so here goes nothing!

Here's the thing about benign tumors. While they may not spread and metastasize, they still can bring about substantial, and sometimes unappreciated, health issues, particularly when they number in the hundreds, or more. In our latest work, we focus on cutaneous neurofibromas in Neurofibromatosis type 1 syndrome

https://www.biorxiv.org/content/10.1101/2022.11.07.515469v1

PSA and reminder: abstract submission deadline for #Dros23 in Chicago is November 17:
https://genetics-gsa.org/drosophila-2023/abstract-submission/

More plotting of flies! I call this one "Fruit fly snow angel"