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Dimos Karamanlis

The latest piece of my PhD work is now published! Check it out at nature.com/articles/s41586-024

We explain how correlated responses in the retinal output may arise when nonlinear receptive fields are stimulated with natural scenes. We think that these concerted responses violate the decorrelation prediction of efficient coding in a cell-type-specific manner in both marmosets and mice.

Summary of visual responses of marmoset retinal ganglion cells stimulated with natural visual scenes with gaze trajectories recorded in actual marmosets.
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Niko Sirmpilatze

As part of this week-long event, I will be hosting a 2-day “Animals in Motion” workshop in London, with the generous support of @SoftwareSaved.

It’s for anyone who wants to get hands-on experience with using open-source software to track animals from video footage and analyse their motion.

Attendance is free of charge, but spots are limited. A small number of travel stipends are available. More info at neuroinformatics.dev/open-soft

#neuroscience #behavior #ethology #neuroethology #python

From: @neuroinformatics
mastodon.online/@neuroinformat

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Yeon Jin Kim

1/ We are excited to share our new manuscript. Here, we provide a nanoscale connectome of the human foveal retina. Our dataset represents the first connectome of any complete neural structure in the human nervous system.

biorxiv.org/content/10.1101/20

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Albert Cardona

"Infrequent strong connections constrain connectomic predictions of neuronal function", Currier and Clandinin
biorxiv.org/content/10.1101/20

Quite the reversal from studies showing that deriving connectomes from correlated neural activity is not accurate because of lacking a unique solution:

"we show that physiology is a stronger predictor of wiring than wiring is of physiology"

#neuroscience #Drosophila #connectomics

Infrequent strong connections constrain connectomic predictions of neuronal function

How does circuit wiring constrain neural computation? Recent work has leveraged connectomic datasets to predict the function of cells and circuits in the brains of many species. However, many of these hypotheses have not been compared with physiological measurements, obscuring the limits of connectome-based functional predictions. To explore these limits, we characterized the visual responses of 91 cell types in the fruit fly and quantitatively compared them to connectomic predictions. We show that these predictions are accurate for some response properties, such as orientation tuning, but are surprisingly poor for other properties, such as receptive field size. Importantly, strong synaptic inputs are more functionally homogeneous than expected by chance, and exert an outsized influence on postsynaptic responses, providing a powerful modeling constraint. Finally, we show that physiology is a stronger predictor of wiring than wiring is of physiology, revising our understanding of the structure-function relationship in the brain. ### Competing Interest Statement The authors have declared no competing interest.

bioRxiv
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Carl T. Bergstrom

The New York Times just discovered parallel computing.

NY Times graphic. Conventional computer: One task starts after another completes AI computing: tasks are divided into small parts and happen at the same time.
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Dimos Karamanlis boosted
Dan Goodman

When I read research papers that are the result of very expensive work (experiments or simulations) I always want to know: how could this project have possibly ended with a null result? And is there an argument in this paper that compares the actual result to this null? If not, I'm very suspicious.

Actually this is a good question to ask about any paper, but the high stakes of super expensive research make it particularly important to ask the question. In my experience, it is surprisingly rarely answered in the paper and I find it hard to believe in these results.

#science #neuroscience

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Niko Sirmpilatze

This was among the most fun projects I’ve worked on! Borrowing some methods from MRI and applying them to whole-brain microscopy data of outstanding quality.

Check out these beautiful (and magnetoreceptive) bird brains!

#anatomy #neuroscience

From: @adamltyson
mastodon.online/@adamltyson/11

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Adam Tyson

New preprint! We built a 3D brain atlas for the migratory and magnetoreceptive Eurasian blackcap.

The atlas is available in @brainglobe and is hopefully the first of many!

Full details:
brainglobe.info/blackcap

Preprint:
biorxiv.org/content/10.1101/20

Short thread:

Overview of the Eurasian Blackcap brain atlas showing annotated brain regions.
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Christoph Schmees

What fast fashion leads to

The spanish paper and online portal EL PAÍS just published a revealing investigation. They endowed used but still good clothes with hidden geolocation tags and deposited the clothes in 15 used clothes bins across Spain. Then they tracked the journeys of the different pieces. It's a long and abysmal story.

english.elpais.com/climate/202

#FastFashion #environment #climate #commodities

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Dimos Karamanlis boosted
bioRxiv Neuroscience

Dendritic Architecture Enables de Novo Computation of Salient Motion in the Superior Colliculus biorxiv.org/content/10.1101/20

Dendritic Architecture Enables de Novo Computation of Salient Motion in the Superior Colliculus

Dendritic architecture plays a crucial role in shaping how neurons extract behaviorally relevant information from sensory inputs. Wide-field neurons in the superior colliculus integrate visual information from the retina to encode cues critical for visually guided orienting behaviors. However, the principles governing how these neurons filter their inputs to generate appropriate responses remain unclear. Using viral tracing, two-photon calcium imaging, and computational modeling, we show that wide-field neurons receive functionally diverse inputs from twelve retinal ganglion cell types, forming a layered, type-specific organization along their dendrites. This structured arrangement allows wide-field neurons to multiplex salient motion cues, selectively amplifying movement and suppressing static features. Computational models reveal that the spatial organization of dendrites and inputs enables the selective extraction of behaviorally relevant stimuli, including de novo computations. Our findings underscore the critical role of dendritic architecture in shaping sensory processing and neural circuit function. ### Competing Interest Statement The authors have declared no competing interest.

bioRxiv
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Dimos Karamanlis boosted
Albert Cardona

Book: Mathematics in Biology, by Markus Meister, Kyu Hyun Lee, and Ruben Portugues.
mathinbio.com/

@mameister4 has a blog entry on why they decided to write the book:
markusmeister.com/2025/02/20/w

Interestingly:

• The web site offers value-added materials, for example sample curricula, and the code for generating every figure in the book.
• The book contains many exercises, but no solutions. We invite student readers to produce such solutions and we will publish the best ones on this site with author credit.

Looks like a long-running project to support and engage the broader community – and it's been 12 years in the making!

#mathematics #mathbio #math #biology

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Sainsbury Wellcome Centre

What drives decision-making in competitive environments?

SWC research teams led by @jerlich and Ann Duan explore multi-agent strategies and dynamical models in a new study.

Read more: sainsburywellcome.org/web/blog

Image of octagon arena.
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EPFL

Hello, Fediverse! Here’s our official #Introduction! 📢
EPFL is now on Mastodon with its very own instance: social.epfl.ch. We're excited to welcome you to this new space to discuss research, education, and innovation.
See you soon on #Mastodon! #EPFL 🚀
go.epfl.ch/mastodon-en

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bioRxiv Neuroscience

Mice dynamically adapt to opponents in competitive multi-player games biorxiv.org/content/10.1101/20

Mice dynamically adapt to opponents in competitive multi-player games

Competing for resources in dynamic social environments is fundamental for survival, and requires continuous monitoring of both 'self' and 'others' to guide effective choices. Yet our understanding of value-based decision-making comes primarily from studying individuals in isolation, leaving open fundamental questions about how animals adapt their strategies during social competition. Here, we developed an ethologically relevant multi-player game, in which freely-moving mice make value-based decisions in a competitive spatial foraging task. We found that mice integrate real-time spatial information about 'self' and the opponent to flexibly shift their preference towards safer, low-payout options when appropriate. Analyses of mice and reinforcement learning agents reveal that these behavioural adaptations cannot be explained by simple reward learning, but are instead consistent with optimal decision strategies guided by opponent features. Using a dynamical model of neural activity, we found that in addition to opponent effects, decisions under competition were also noisier and more sensitive to initial conditions, generating testable predictions for neural recordings and perturbations. Together, this work reveals a fundamental mechanism for competitive foraging, and proposes novel quantitative frameworks towards understanding value-based decision-making in a fast-changing social environment. ### Competing Interest Statement The authors have declared no competing interest.

bioRxiv
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Current Biology

Eye saccades align optic flow with retinal specializations during object pursuit in freely moving ferrets cell.com/current-biology/fullt

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Konrad Kording

Announcing a new week-long program for young computational neuroscience/ behavior professors to talk about rigorous science, mentoring, lab management, and networking in a stunning retreat setting. Do great science as a community and have fun doing so.

As assistant professors in neural, computational and behavioral science, it was hard to learn how to do good science, mentor students, navigate administration, while having fun. New 1 week academy for young professors: join us August 23-30, 2025 in Kingston, ON, Canada.

Learn more and apply here: lnkd.in/ecaatvc8

Great lecturers for key skills: Hannah Bayer, Patrick Mineault, Yael Niv, Megan Peters, and your hosts Gunnar Blohm and Konrad Kording, and of course networking with an amazing group of 30 other professors.

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Dan Goodman

What's the right way to think about modularity in the brain? This devilish 😈 question is a big part of my research now, and it started with this paper with @GabrielBena finally published after the first preprint in 2021!

nature.com/articles/s41467-024

We know the brain is physically structured into distinct areas ("modules"?). We also know that some of these have specialised function. But is there a necessary connection between these two statements? What is the relationship - if any - between 'structural' and 'functional' modularity?

TLDR if you don't want to read the rest: there is no necessary relationship between the two, although when resources are tight, functional modularity is more likely to arise when there's structural modularity. We also found that functional modularity can change over time! Longer version follows.

#Neuroscience #CompNeuro #ComputationalNeuroscience

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Terence Tao

The behavior of a high-dimensional dynamical system can, very roughly speaking, be divided into two regimes. The first is what one might call the "effective dynamics" regime, in which the complex, high-dimensional dynamics can be well approximated (in the observables that one particularly cares about, at least) by lower-dimensional effective equations or models that emerge from the more fundamental laws of motion, and are easier to understand and analyze. A classical example is the laws of thermodynamics, which can effectively govern (some of the) macroscopic behavior of a large number of interacting particles, due to mixing effects that greatly simplify the impact of most of the degrees of freedom. Another example from physics is Hooke's law, that asserts that an elastic object, such as a spring, exerts a linear restoring force to push it in the direction of its equilibrium. Similar linear restoring force phenomena can be seen across the sciences (such as climate science, biology, economics, or even political science): not as fundamental laws of nature, but as empirically observable laws that emerge from more fundamental ones. Such effective laws can provide a valuable amount of long-term stability, predictability, and simplification to the dynamical understanding of many real-world complex systems. (1/4)

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Zeke Hausfather

Great (and scary) visualization of 2024 daily temperatures compared to prior years by the BBC today. Evocative of the iconic Joy Division album cover from 1979: bbc.com/news/articles/cd7575x8

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Dimitris Kontopoulos

Thrilled to share my first main #paper from my #EMBO #postdoc fellowship that is out today in #FunctionalEcology: besjournals.onlinelibrary.wile 🥳

Read on to learn about the #evolution of #torpor among #mammals and #birds!

🧵 1/12

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Anna Dorofeeva

Are any computer scientists here on Mastodon working in Visual Computing, or Computer Vision? I'm looking for a collaborator to work on the visualisation of medieval handwriting as movement. Would be grateful for re-posts!

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