Albert Cardona @albertcardona@qoto.org

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 #cerebellum #connectomics. Those must be the prettiest Purkinje cell renderings since the century-old famous ones from Cajal. This time with synapses though!
#neuroscience

"Structured cerebellar connectivity supports resilient pattern separation" Nguyen, Thomas et al. in @darbly's lab https://www.nature.com/articles/s41586-022-05471-w

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."

#cerebellum #connectomics #neuroscience #science #vEM #volumeEM #NeuralBetwork

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: https://www.janelia.org/you-janelia/conferences/neuro-evo-a-comparative-approach-to-cracking-circuit-function-iii

"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."

#NeuroEvo #Janelia #HHMI #conference #science #academia #neuroscience #DevBio #connectomics #connectome

“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 #connectomics, like the chameleons of the genus #Brookesia https://en.m.wikipedia.org/wiki/Brookesia

#herpetology #lizards #frogs #Madagascar #nature #neuroscience

For neuroscientists attending #sfn22: don’t miss the poster by Mitya Chklovskii’s group describing the completion status of the whole brain #connectome of the fairy wasp #Megaphragma, 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 #wasp 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. https://www.sciencedirect.com/science/article/pii/S1467803911000946

#neuroscience #connectomics

Have you visited the #FlyWire website yet? Both for helping proofread and analyze the whole #Drosophila brain #connectome, or simply to admire the beautiful renderings of neuronal arbors: https://join.flywire.ai

(See also the #VirtualFlyBrain for #ontology-driven navigation of the fly brain, and access to images of genetic driver lines, and more: https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?id=VFB_00101567&i=VFB_00101567 )

Wish I had time or resources to create such a beautiful landing page for the larval central nervous system. The #connectome of the whole larval brain is coming soon. For now, see the #vEM images and some ~3,000 published neurons in this #CATMAID server: https://l1em.catmaid.virtualflybrain.org/?pid=1&zp=108250&yp=82961.59999999999&xp=54210.799999999996&tool=tracingtool&sid0=1&s0=2.4999999999999996&help=true&layout=h(XY,%20%7B%20type:%20%22neuron-search%22,%20id:%20%22neuron-search-1%22,%20options:%20%7B%22annotation-name%22:%20%22papers%22%7D%7D,%200.6)

#connectomics

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

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

... in which the authors show, using #vEM and #connectomics, that while the nematode #celegans 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.

URL: https://doi.org/10.1016/j.cub.2022.09.065

#readingpapers #science #neuroscience #development

To fill in my profile tags, a thread:

#TrakEM2 is open source software mostly for #connectomics (but found uses well beyond), and provides the means for both manual and automatic montaging and aligning overlapping 2D image tiles (with #SIFT 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 #connectome from #vEM (volume electron microscopy).

#TrakEM2 paper at https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0038011

Git repository at https://github.com/trakem2/

For 3D visualization, #TrakEM2 uses the 3D Viewer https://imagej.net/plugins/3d-viewer/

As software, #TrakEM2 runs as a plugin of #FijiSc https://fiji.sc/ and in fact motivated the creation of the #FijiSc software in the first place, to manage its many dependencies and therefore facilitate distribution to the broader #neuroscience community.

#TrakEM2 was founded in 2005, when terabyte-sized datasets were rare and considered large. The largest dataset that I've successfully managed with #TrakEM2 was about 16 TB. For larger datasets, see #CATMAID below.

Above, my #introduction of interests. Here, who I am, what I do: a neuroscientist at the #MRCLMB and University of Cambridge, UK, studying the neural circuit basis of behavior, originally in #Drosophila but now also in #cephalopods (#pygmysquid #Idiosepius), the lancelet #Amphioxus and other animals. Our main approach: whole brain #connectomics with #vEM (volume electron microscopy) as the basis for computational modeling to guide neuronal activity perturbation and monitoring experiments with #optogenetics and #electrophysiology (#ephys for short).
Once upon a time I founded the #ImageJ -based #TrakEM2 software for image registration and neuronal arbor reconstruction and annotation, which spurred founding the #FijiSc (https://fiji.sc) image processing software, and later the #CATMAID web-based software for #connectomics.
Always open to inquires from prospective students and postdocs, and collaborations.