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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"Structured cerebellar connectivity supports resilient pattern separation" Nguyen, Thomas et al. in @darbly's lab

Spectacular work based on connectomic reconstruction from nanometre-resolution volume electron microscopy and computational modelling that contributes novel findings in cerebellar microcircuitry:

"both the input and output layers of the circuit exhibit redundant and selective connectivity motifs, which contrast with prevailing models. Numerical simulations suggest that these redundant, non-random connectivity motifs increase the resilience to noise at a negligible cost to the overall encoding capacity. This work reveals how neuronal network structure can support a trade-off between encoding capacity and redundancy, unveiling principles of biological network architecture with implications for the design of artificial neural networks."

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."

“The natural history of Madagascar”, a new book including all those teeny tiny frogs and lizards—chameleons, in particular—with so much potential for whole-brain , like the chameleons of the genus


Dr Mark D. Scherz (He/Him)  
HOT OFF THE PRESS: The New Natural History of Madagascar! At >2000 pages over two volumes, with >600 contributing authors, it sets a new benc...

For neuroscientists attending : don’t miss the poster by Mitya Chklovskii’s group describing the completion status of the whole brain of the fairy wasp , of expected completion early in 2022. Find the poster tomorrow Monday morning, number 328.16 / YY35.

Mitya kindly shared the poster image publicly elsewhere.

This tiny is famous for being the size of a large paramecium (a unicellular organism) and for enucleating the vast majority of its central neurons while pupating. The adult has less that 10,000 neurons in its central brain yet it isn’t missing any organ or body part. See the paper that jumpstarted this effort:

Polilov AA. The smallest insects evolve anucleate neurons. Arthropod structure & development. 2012 Jan 1;41(1):29-34.

Have you visited the website yet? Both for helping proofread and analyze the whole brain , or simply to admire the beautiful renderings of neuronal arbors:

(See also the for -driven navigation of the fly brain, and access to images of genetic driver lines, and more: )

Wish I had time or resources to create such a beautiful landing page for the larval central nervous system. The of the whole larval brain is coming soon. For now, see the images and some ~3,000 published neurons in this server: l1em.catmaid.virtualflybrain.o)

Casey Schneider—Mizell studies the cerebral with at the Allen Brain Institute, and develops software for mapping and analyzing in very large image volumes with nanometer resolution measuring over a cubic millimeter.


Casey Schneider-Mlzell  
Time for an #introduction. Nervous systems — yours, mine, those of mice, fish, and insects and worms — are made up of populations of different kind...

"Post-embryonic remodeling of the C. elegans motor circuit" by Ben Mulcahy et al. 2022 (Mei Zhen's lab

... in which the authors show, using and , that while the nematode nervous system grows from ~200 neurons in the hatchling to ~300 in the adult, the addition of new neurons doesn't disrupt existing motor function, but new circuits are formed that endow the animal with new behaviors such as bending.

Interestingly, in the course of larval maturation one neuron type inverts its polarity: what was the dendrite becomes the axon, and viceversa. And this is accomplished not with retraction and regrowth of the arbor, but rather, by flipping the synapses in situ.


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.

Above, my of interests. Here, who I am, what I do: a neuroscientist at the and University of Cambridge, UK, studying the neural circuit basis of behavior, originally in but now also in ( ), the lancelet and other animals. Our main approach: whole brain with (volume electron microscopy) as the basis for computational modeling to guide neuronal activity perturbation and monitoring experiments with and ( for short).
Once upon a time I founded the -based software for image registration and neuronal arbor reconstruction and annotation, which spurred founding the ( image processing software, and later the web-based software for .
Always open to inquires from prospective students and postdocs, and collaborations.

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