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NeurOnToSomethingLatest post in a <a href="https://mas.to/tags/Neuro" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Neuro</a> <a href="https://mas.to/tags/Science" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Science</a> <a href="https://mas.to/tags/Fiction" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Fiction</a> <a href="https://mas.to/tags/WorldBuilding" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#WorldBuilding</a> projectThe <a href="https://mas.to/tags/Brane" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Brane</a> <a href="https://mas.to/tags/Connectome" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Connectome</a>: Basically Fetid<a href="https://mas.to/tags/astrobiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#astrobiology</a> <a href="https://mas.to/tags/cosmology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#cosmology</a> <a href="https://mas.to/tags/abiogenesis" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#abiogenesis</a> <a href="https://mas.to/tags/fermi_paradox" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#fermi_paradox</a> <a href="https://neurontosomething.wordpress.com/2024/09/29/brane-connectome-project-basically-fetid/" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://neurontosomething.wordpress.com/2024/09/29/brane-connectome-project-basically-fetid/</a>

Gaspar JekelyWe have now published a new and massively extended/reworked preprint of the whole-body <a href="https://biologists.social/tags/Platynereis" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Platynereis</a> larval <a href="https://biologists.social/tags/connectome" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#connectome</a> with over 50 figures<a href="https://www.biorxiv.org/content/10.1101/2024.03.17.585258v1" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://www.biorxiv.org/content/10.1101/2024.03.17.585258v1</a>All the analyses, plots and figures should be reproducible in <a href="https://biologists.social/tags/rstats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rstats</a> with the code provided:<a href="https://zenodo.org/doi/10.5281/zenodo.10825370" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://zenodo.org/doi/10.5281/zenodo.10825370</a><a href="https://bird.makeup/users/zenodo_org" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@zenodo_org</a> by querying our public <a href="https://biologists.social/tags/CATMAID" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CATMAID</a> database:<a href="https://catmaid.jekelylab.ex.ac.uk" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://catmaid.jekelylab.ex.ac.uk</a><a href="https://biologists.social/tags/neuroscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#neuroscience</a> <a href="https://mander.xyz/c/biology" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@biology</a> <a href="https://biologists.social/tags/volumeEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#volumeEM</a> <a href="https://biologists.social/@biorxivpreprint" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@biorxivpreprint</a>

Albert CardonaMy science outreach take on our work mapping and analyzing the <a href="https://mathstodon.xyz/tags/connectome" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#connectome</a> of the <a href="https://mathstodon.xyz/tags/Drosophila" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Drosophila</a> larval brain, this time in catalan: <a href="https://blocs.mesvilaweb.cat/cardona/el-cervell-per-a-que/?vlw=1" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://blocs.mesvilaweb.cat/cardona/el-cervell-per-a-que/?vlw=1</a><a href="https://mathstodon.xyz/tags/CadaDiaCi%C3%A8ncia" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CadaDiaCiència</a> <a href="https://mathstodon.xyz/tags/catal%C3%A0" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#català</a> <a href="https://mathstodon.xyz/tags/ci%C3%A8ncia" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ciència</a> <a href="https://mathstodon.xyz/tags/neurobiologia" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#neurobiologia</a>

Albert CardonaToday the peer-reviewed version of our preprint is out:"The <a href="https://mathstodon.xyz/tags/connectome" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#connectome</a> of an insect brain" <a href="https://www.science.org/doi/10.1126/science.add9330" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://www.science.org/doi/10.1126/science.add9330</a>Congrats to co-first authors Michael Winding and Benjamin Pedigo, and to all our lab members and collaborators who made this work possible over the years. A journey that started over 10 years ago–and yet this is but a new beginning. So much more to come.See my <a href="https://mathstodon.xyz/tags/tootprint" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#tootprint</a> on the preprint from back in the Autumn: <a href="https://mathstodon.xyz/@albertcardona/109422190525090990" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://mathstodon.xyz/@albertcardona/109422190525090990</a>The data is available both as supplements and directly via <a href="https://mathstodon.xyz/tags/CATMAID" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CATMAID</a> thanks to hosting by the <a href="https://mathstodon.xyz/tags/VirtualFlyBrain" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#VirtualFlyBrain</a>: <a href="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" rel="nofollow noopener noreferrer" translate="no" target="_blank">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</a>)(The "Winding, Pedigo et al. 2023" annotation listing all included neurons will appear very soon in an upcoming update.)<a href="https://mathstodon.xyz/tags/neuroscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#neuroscience</a> <a href="https://mathstodon.xyz/tags/connectomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#connectomics</a> <a href="https://mathstodon.xyz/tags/Drosophila" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Drosophila</a> <a href="https://mathstodon.xyz/tags/DrosophilaLarva" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#DrosophilaLarva</a>

Albert CardonaNext, we explored the <a href="https://mathstodon.xyz/tags/Drosophila" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Drosophila</a> larval <a href="https://mathstodon.xyz/tags/connectome" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#connectome</a> with multi-hop signal cascades (left) that extended across synapses up to a depth of 5. We sorted neurons into labelled lines and multisensory (right).Neurons were considered to receive sensory input when visited in most cascade iterations.The majority of brain neurons integrate from all sensory types, but a few neurons integrated from only one sensory modality (labelled line) or from a combination.<a href="https://mathstodon.xyz/tags/neuroscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#neuroscience</a> <a href="https://mathstodon.xyz/tags/connectomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#connectomics</a>5/

Albert CardonaHaving split the <a href="https://mathstodon.xyz/tags/Drosophila" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Drosophila</a> larval brain <a href="https://mathstodon.xyz/tags/connectome" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#connectome</a> into 4 types of edges, hierarchical spectral clustering defined about 90 groups of neurons.Remarkably, clusters defined by connectivity alone were internally consistent for other features, such as neuron morphology or function.Clusters were sorted from sensory neurons (SNs) to descending neurons (DNs) using the Walk-Sort algorithm. To the right, example clusters with intracluster morphological similarity score using NBLAST.4/

Albert CardonaOur analysis of the <a href="https://mathstodon.xyz/tags/Drosophila" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Drosophila</a> larval brain starts by recognizing that neurons are polarized: 95.5% of all brain neurons present clearly segregated axons and dendrites.In the <a href="https://mathstodon.xyz/tags/connectome" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#connectome</a>, we found 66% axo-dendritic synapses, 26% axo-axonic, 6% dendro-dendritic and 2% dendro-axonic.This matters because inputs onto dendrites contribute to the integration function of a neuron; inputs onto an axon modulate its output. Analysing them separately makes sense.<a href="https://mathstodon.xyz/tags/neuroscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#neuroscience</a> <a href="https://mathstodon.xyz/tags/connectomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#connectomics</a> 3/

Albert CardonaOur map of the <a href="https://mathstodon.xyz/tags/Drosophila" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Drosophila</a> larval brain <a href="https://mathstodon.xyz/tags/connectome" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#connectome</a> is complete, with all inputs and all outputs, and everything in between: all polysynaptic pathways from sensory neurons all the way to brain output neurons, across both brain hemispheres. 2/<a href="https://mathstodon.xyz/tags/neuroscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#neuroscience</a> <a href="https://mathstodon.xyz/tags/connectomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#connectomics</a>

Albert Cardona3,013 neurons, half a million synapses: the complete <a href="https://mathstodon.xyz/tags/connectome" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#connectome</a> of the whole <a href="https://mathstodon.xyz/tags/Drosophila" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Drosophila</a> larval brain!Winding, Pedigo et al. 2022. "The connectome of an insect brain" <a href="https://www.biorxiv.org/content/10.1101/2022.11.28.516756v1" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://www.biorxiv.org/content/10.1101/2022.11.28.516756v1</a>We’ve mapped and analysed its circuit architecture, from sensory neurons to brain output neurons, as reconstructed from volume electron microscopy, and here is what we found. 1/<a href="https://mathstodon.xyz/tags/neuroscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#neuroscience</a> <a href="https://mathstodon.xyz/tags/connectomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#connectomics</a> <a href="https://mathstodon.xyz/tags/vEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#vEM</a> <a href="https://mathstodon.xyz/tags/volumeEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#volumeEM</a>

Albert CardonaThe web-based open source software <a href="https://mathstodon.xyz/tags/CATMAID" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CATMAID</a> was devised as "google maps but for volumes". Documentation at <a href="https://catmaid.org" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://catmaid.org</a> and source code at <a href="https://github.com/catmaid/CATMAID/" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://github.com/catmaid/CATMAID/</a>Modern <a href="https://mathstodon.xyz/tags/CATMAID" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CATMAID</a> enables hundreds of <a href="https://mathstodon.xyz/tags/neuroscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#neuroscience</a> researchers world wide to collaboratively map neuronal circuits in large datasets limited only by bandwidth and server-side storage to map and analyse a whole brain <a href="https://mathstodon.xyz/tags/connectome" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#connectome</a>.See the <a href="https://mathstodon.xyz/tags/Drosophila" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Drosophila</a> larval CNS at the <a href="https://mathstodon.xyz/tags/VirtualFlyBrain" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#VirtualFlyBrain</a> server: <a href="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" rel="nofollow noopener noreferrer" translate="no" target="_blank">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</a>)

Albert Cardona<a href="https://mathstodon.xyz/tags/introduction" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#introduction</a> To fill in my profile tags, a thread:<a href="https://mathstodon.xyz/tags/TrakEM2" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#TrakEM2</a> open source software mostly for <a href="https://mathstodon.xyz/tags/connectomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#connectomics</a>, and supports manual and automatically montaging and aligning overlapping 2D image tiles (with <a href="https://mathstodon.xyz/tags/SIFT" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#SIFT</a> features and rigid or elastic transformation models), and reconstructing by painting volumes or tracing branched neuronal arbors neurons plus synapses to map a <a href="https://mathstodon.xyz/tags/connectome" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#connectome</a> from <a href="https://mathstodon.xyz/tags/vEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#vEM</a> (volume electron microscopy).See: <a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0038011" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0038011</a>Git repository at: <a href="https://github.com/trakem2/" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://github.com/trakem2/</a>

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