Davi Bock

From @bdpedigo.bsky.social: a super efficient, highly reliable, and very generalizable method for mesh structure classification, applied here to spine detection across basically every synapse onto a cell in the MICRoNS dataset.

GitHub - saalfeldlab/lens-correct: Correcting lens-distortion in confocal stacks Correcting lens-distortion in confocal stacks. Contribute to saalfeldlab/lens-correct development by creating an account on GitHub.

If your imaging system has poorly characterized constant distortions leading to chromatic aberration, shoddy stitching, or false measurements (the answer is likely yes), you may want to give this tool a try. Native installers for Linux, Mac, Win under Releases github.com/saalfeldlab/...

Historic U.S. marine lab parts ways with the University of Chicago After a 12-year affiliation intended to address financial woes, the Marine Biological Laboratory returns to independence

As money woes hit the University of Chicago, the oldest private marine laboratory in the United States is striking out on its own. https://scim.ag/4trAN3l

Please spread the word:

We invite applications to a two-week Computational Biology workshop in Singapore, June 14-27.

This NSF-funded workshop brings together 16-20 US grad students with international peers.
Apply by March 21: compbioasia.net
🧵 Details below:

A line plot with the numbers of NSF awards for fiscal years 2021-2026. The curve for fiscal year 2026 is quite a bit lower than those for 2021-2025 while the curve for fiscal year 2026 (in red) is much lower than all through the same date.

But, as they say, there is no time like the present

[OK, maybe the 1930s if you want to nitpick]

But, with some data wrangling, my first NSF Funding Curves!

2/3

beautiful protist ExM images here from @dudinlab.bsky.social and @gautamdey.bsky.social

Want to come do a postdoc with us?

We’re interested in how sensorimotor function is carried out by the cells and circuits of the spinal cord. We have an awesome team, lots of cool techniques, and we’re open to new ideas/approaches/connections. Get in touch!

Georges Borchardt, 97, Dies; Literary Agent Championed Wiesel’s ‘Night’

I usually hesitate to post obituaries but this one, of my literary agent, Georges Borchardt, born in 1928, is so unusual that it deserves to be widely shared.
An incredible 20th century life
www.nytimes.com/2026/01/20/o...

CytoTape in a neuron

Our CytoTape work is published today in Nature @nature.com! CytoTape is a genetically encoded, flexible, intracellular protein tape recorder for spatiotemporally scalable and multiplexed recording of cellular activities continuously across weeks in vitro and in vivo. www.nature.com/articles/s41...

I had no idea Leiber had become so obscure!

Scatter plot with eye sight acuity (measured in cycles per degree) on the y-axis and eye diameter (in mm) on the x-axis. Birds tend to have higher acuity than mammals at a given eyesight, except anthropoid primates (monkeys and apes) that outperform most birds, except for a few raptors. Some birds of prey (falcons, eagles) exhibit the highest recorded acuity. Corvids cluster between other birds and anthropoids, showing higher acuity than would be expected.

Another bit on eye-sight: I've put together a plot on visual acuity in birds and mammals. Interestingly, corvids seem to have acuity that is a lot better than expected for their eye size/passerines in general. Is anyone aware of structural peculiarities of corvid eyes that might explain that? 🧪🪶

Neuroscience, BRAIN Initiative gain budget in ‘bad’ NIH funding bill The bill goes before the House of Representatives today and outlines increases for neuroscience-related research—including a 33 percent increase to the BRAIN Initiative—but maintains a multiyear…

The bill includes a 33 percent budget increase for the NIH’s BRAIN Initiative, which has faced significant funding cuts over the past two years.

By @avaskham.bsky.social

#neuroskyence

www.thetransmitter.org/funding/neur...

The winner of the 2026 Pradel Research Award is H. Sebastian Seung of @princetonneuro.bsky.social! He is being honored for for transformative advances in computational neuroscience. Learn more about his discoveries: www.nasonline.org/award/pradel... #NASaward #neuroscience

What's the relation between voltage and calcium in dendrites? Xiang Wu studied this in CA2 hippocampal pyramidal cells in behaving mice. www.biorxiv.org/content/10.6...

This course looks great. Amazing organisms + friendly and highly expert instructors, several of whom I have had the privilege of getting to know during my time so far here in Heidelberg. Strong recommend!

Please apply. Amazing opportunity to dive into connectomics datasets for research, educational initiatives, outreach and whatever else your heart desires. Feb 2nd deadline.

Scientific Workflows Developer The European Molecular Biology Laboratory (EMBL) is Europe’s life sciences laboratory – an intergovernmental organisation with more than 110 independent research groups and service teams covering the ...

Big news! The Data Management team/Data Science Centre at EMBL (i.e. my team) is hiring for a position based in Heidelberg (but working across all sites!). We are looking for a scientific workflows developer that will focus on multimodal pipelines. embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

Thank you!!! This was a whole lot of work by a whole lot of people!!!!

Poster of the EM course in Naples with marine samples. The Electron Microscopy Hands-On Course: sample preparation and imaging of marine environmental samples arises from a very strong and active collaboration between the Stazione Zoologica Anton Dohrn and the EMBL in Heidelberg. The aim of the course is to provide a theoretical and practical training on electron microscopy starting from the basics to the preparation of samples with high pressure freezing and image acquisition using TEM and SEM.

If you are interested in electron microscopy, registration is still open for the

"Electron Microscopy Hands-On Course: sample preparation and imaging of marine environmental samples"

at Stazione Zoologica in Naples.

WIth great teachers from Naples […]

[Original post on biologists.social]

How about there are _no_ "fundamental" computational units -- these are (useful!) abstractions to help us deal with the computational density of biological matter, which operates across scales. Occasionally, but not always, dynamics from a finer scale unit matter a lot to a courser one.

How do neural circuits generate the walking rhythm?

Using connectome simulations, @sarahpugly.bsky.social found a minimal central pattern generator (CPG) that produces oscillations in leg motor neurons. Same circuit motif for each 🪰 leg.

w @bingbrunton.bsky.social

www.biorxiv.org/content/10.1...

The cryo cyclical multiplexing expansion microscopy (Cy-ExM) preprint from
@seweryn-galecki.bsky.social , @kevin-dean.bsky.social et al is online.

20 targets across an entire cell. Mr. Snouty also joined the fun.

www.biorxiv.org/content/10.6...

my modest collection of flies with WIDE heads 🙇

a hammer-headed Richardia (Ecuador),
a stalk-eyed Chaetodiopsis (Mozambique),
a pointy-eyed Ophthalmoptera (Colombia),
and an antlered Richardia (Colombia)

why though? male-male competition? sexual selection? chime-in if you know!

Organelles do NOT have a single uniform pH.
And if you think they must, because “protons diffuse fast,” this paper is for you.
A thread on why that assumption is wrong; and what we found instead. 🧵 1/n

Schematic of how ER-EPG plasticity enables the bump of activity in EPGs to accurately track visual cues. As a fly makes a counter-clockwise turn (top to bottom) it will view visual cues (e.g. the sun) from a new angle and the EPG activity bump (red) will swing clockwise around the network by integrating self motion signals with these visual inputs. When the fly faces a different angle, distinct visual ER neurons are active. Plasticity forms a trough of weak synapses (large circles - strong synapses, small circles - weak synapses) that allow ER neurons with distinct visual tuning to move the EPG bump via disinhibition.

*First preprint from our lab* !!!!!
How does the brain learn to anchor its internal sense of direction to the outside world? 🧭
led by Mark Plitt @markplitt.bsky.social & Dan Turner-Evans, w/ Vivek Jayaraman:
“Octopamine instructs head direction plasticity” www.biorxiv.org/content/10.6...
Thread ⬇️

Two nerve nets are formed in Hydra vulgaris: the endodermal (cyan) and the ectodermal (purple) net. (B) Intraepithelial neurons are randomly scattered between the epithelial cells of the two germ layers. (C) Two types of connections have been found between Hydra’s neurons. (D) Endodermal neurons are in physical touch with each other by forming neural handshakes by digiform endings, which get intertwined. (E) In other places, clusters of vesicles of different types can be released to mediate volume transmission between neurons and between neurons and other cells.

Our dispatch:

https://www.sciencedirect.com/science/article/pii/S0960982225014691

on the recent Hydra volume EM paper by Zhang, Rafa Yuste and colleagues:

#connectomics, without synapses

https://www.sciencedirect.com/science/article/pii/S0960982225013090

#neuroscience

🧠🪰 The adult Drosophila brain connectome now gives us a complete wiring diagram of ~140k neurons. But a wiring diagram alone isn’t understanding.

How is this massive network organized?

Our paper tackles that question by mapping community structure across the entire fly brain. 1/

Spatial and morphological organization of mitochondria in neurons across a connectome Neuronal function depends on mitochondria, but little is known about their organization across neurons. Using an electron microscopy Drosophila connectome, we uncovered quantitative rules governing th...

A paper from my PhD lab is on Science! This is a really cool new way to utilize EM connectome datasets. Congrats to the team!
www.science.org/doi/10.1126/...

Love the caption of Fig. 3 in this impressive preprint:
"A Goodsell-esque 3D orthogonal rendering of an IsoNet2-processed FIB-milled tomogram of C. reinhardtii"
doi.org/10.64898/202...
Since I am no expert, what does the cryoET community think of IsoNet? @cellarchlab.com
doi.org/10.1038/s414...