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Neuro-evo conference at HHMI Janelia on May 15-18, 2023. Join us for the third edition!

Application deadline: Jan 27 (11:59 p.m. EST) 2023.

Apply here:

"Historically, with the study of the most convenient animal models —from the giant axon of the squid and the lobster's stomatogastric circuits to Aplysia's synapses and C. elegans' circuits — neuroscientists revealed some of the operating principles of the nervous system, which were then found to apply broadly across phyla. The third instalment of this meeting will once again bring together neuroscientists working on a broad diversity of animal models in an effort to compare circuits across phyla as a means to crack their function."

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Have you discovered the image processing forum yet?

Featuring tutorials, requests for guidance, help, discussion of new features and documentation for open source software and many more.

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The web-based open source software was devised as "google maps but for volumes". Documentation at and source code at

Modern enables hundreds of researchers world wide to collaboratively map neuronal circuits in large datasets, e.g., 100 TB or larger, limited only by bandwidth and server-side storage. The goal: to map and analyse a whole brain .

Running client-side on and server-side on , it's a pleasure to use–if I may say so–and easy to hack on to extend its functionality with further widgets.

The first minimally viable product was produced in 2007 by Stephan Saalfeld (what we now refer to, dearly, as "Ice Age CATMAID), who demonstrated to us all that the web, and javascript, where the way to go for distributed, collaborative annotation of large datasets accessed piece-wise. See the original paper:

See also public instances at the particularly under "tools - CATMAID - hosted EM data such as this first instar larval volume of its complete nervous system l1em.catmaid.virtualflybrain.o)

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To fill in my profile tags, a thread:

is open source software mostly for (but found uses well beyond), and provides the means for both manual and automatic montaging and aligning overlapping 2D image tiles (with features and rigid or elastic transformation models), and then reconstructing with mostly manual means–by painting with a digital brush–the volumes of structures of interest, as well as trace the branched arbors of e.g., neurons and annotate their synapses, therefore mapping a from (volume electron microscopy).

paper at

Git repository at

For 3D visualization, uses the 3D Viewer

As software, runs as a plugin of and in fact motivated the creation of the software in the first place, to manage its many dependencies and therefore facilitate distribution to the broader community.

was founded in 2005, when terabyte-sized datasets were rare and considered large. The largest dataset that I've successfully managed with was about 16 TB. For larger datasets, see below.

@callieconnected @albertcardona. Noise is complex. A system’s robustness to noise can be improved in different ways, for example by minimizing variability or increasing signal size and separability.

We think the network we mapped is able to do this because neurons sample more redundantly than expected from specific inputs. Those inputs may be less noisy or convey more relevant information. This is interesting because prevailing models assume random, non-specific sampling, which is thought to optimize the amount of information a network can encode.

If interested, this review may be useful:

The offers fully funded PhD studentships. Come join us!

Deadline: December 1st, 2022 (six days left).

Have a look at the projects listed for the Neurobiology Division (where Marta Zlatic, Greg Jefferis, Bill Schafer, Marco Tripodi, and many others, including myself).

List of projects:

How to apply:

Great paper: a droplet assay to encapsulate single micron-sized algae to study long-term .
by Bentley et al. and @micromotility
A thread.

Hi all,

I'm a postdoc in #computerscience at the University of #Vienna, working in #algorithms.

I am interested in the design, analysis, and experimental evaluation of algorithms and especially in #AlgorithmEngineering , which means that I am studying how algorithms perform in practice and how to make them better and/or faster in real-world scenarios. I particularly like dynamic algorithms, which can also deal with changes in the data and don't have to recompute from scratch.


Hi all! I’m a neuroscientist and cerebellum enthusiast doing a postdoc at Western University, CAN. I did my PhD in Oxford, UK on neurotransmitter changes in the cerebellum and postdoc-ed in Cambridge.

I want to find out what the cerebellum contributes to cognition and how it interacts with the cortex. For that, I use imaging (fMRI, MRS) & computational techniques (NLP, ML) & brain stim (tDCS).

Follow me for a dose of cerebellum news and science memes!
#cerebellum #neuroscience #introduction

Some very cool science from
Scott Hensley's lab published today in Science points a way to a potential universal #flu vaccine. If this works in people, this could prime us against all known flu hemagglutinins, dramatically lowering the risks flu pandemics pose.

I’m a bit late to the game, but now out, in a more final form:

Tri Nguyen, @lathomas42, and our team found neurons sample inputs redundantly and selectively in ways that may help make the network more robust with a minimal loss of encoding capacity.

@albertcardona Thank you for so kindly describing Tri Nguyen’s and @lathomas42’s paper. Indeed, Purkinje cells are amongst the most “elegant and luxurious” extracted out of our EM data.

Folks can see more for themselves here:

📢Latin Americans doing a PhD in Computer Science📢

Apply by Jan 11, 2023 for a Google PhD fellowship:
$15K in funding and mentorship from a Google researcher!

👇🏾👇🏾Read more below 👇🏾👇🏾

One of the two first authors, Logan Thomas @lathomas42 is on mastodon, as is the senior author Wei Lee @darbly. Welcome! And what a spectacular paper on . Those must be the prettiest Purkinje cell renderings since the century-old famous ones from Cajal. This time with synapses though!

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👋 Hello from #Zurich!

I'm a researcher working at the intersection of #neurosciene and #ai. Before joining Google's #connectomics team earlier this year, I did my PhD advised by @jakhmack on simulation-based Inference (#sbi).

Excited to see Mastodon gaining momentum!

@brembs @HeedLab @bohaceklab @eLife @richardsever I tend to agree that the incentives are in the wrong place. Public funders should incentivize behaviors that support scientific advance rather than the careers of individual scientists (as in, CNS publications). Open Science is non-trivial in cost and effort and until it is supported and valued for funding/hiring decisions, it will be hard to have systemic change

I will start recruitment soon, but for now, I'm looking for
- a lab manager who will build the new lab with me (namely the central pillar of my Dresden lab)
- a postdoctoral fellow interested in comparing tissue mechanics of organoids across species.
Please reach out to me. 3/

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Introductory post: I'm an entomologist/evolutionary biologist that's interested in the evolution of Hymenoptera 🐝 🐜 , in particular gall inducing/ parasitic wasps. Currently I'm a Marie Curie fellow at the University of Edinburgh, using phylogenomics 🧬 , community ecology 💻 , and morphological taxonomy 🔬 to figure out who's who, and who eats who in tritrophic systems consisting of 🌹 -> 🌹gall wasps->their natural enemies.

Our gigantic pub on the arthropod associates of 155 North American cynipid oak galls is now freely available! We report rearing records from 527,306 galls representing 201 different oak gall types collected from 32 oak tree species in US + Canada.

#introductions: Hi, I'm a junior #professor in Neurocognitive Developmental Psychology, doing #research on #attention, #emotion and #social #development using #psychology and #neuroscience methods such as #eye-tracking and #EEG. I'm also an #OpenScience enthusiast and a #MotherInScience

Honest question. A large portion of the #neuroscience community just moved from bird to mammoth. A massive shift. What if we all decided to destroy the broken publishing system by only submitting to @eLife from now on? What would happen? Would eLife collapse in an instant? Would its impact factor rise astronomically? Where would we publish all the stuff that gets rejected from them? @richardsever

The Journal of Open Source Software is a developer friendly, diamond/platinum open access journal for research software packages.

Committed to publishing quality research software with zero article processing charges or subscription fees.

Just wanted to share a link to our #LongCOVID mechanisms, risk factors and recovery review that's just come out in Experimental Physiology. It was such a pleasure to work with so many excellent scientists on this - most of whom I haven't yet bumped into on mastodon.

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Qoto Mastodon

QOTO: Question Others to Teach Ourselves
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All cultures welcome.
Hate speech and harassment strictly forbidden.