Philip Hubbard<p>Here's a <a href="https://fediscience.org/tags/MicroscopyMonday" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>MicroscopyMonday</span></a> segmentation of some neurons from the optic lobe, or visual processing area of the <a href="https://fediscience.org/tags/Drosophila" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Drosophila</span></a> fruit fly's brain. The <a href="https://fediscience.org/tags/connectome" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>connectome</span></a> for the full optic lobe was released in 2024 by <a href="https://fediscience.org/tags/HHMIJanelia" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>HHMIJanelia</span></a>, Google, and the University of Cambridge, with support from the Wellcome Trust.</p>
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#connectome
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Albert Cardona<p><span class="h-card" translate="no"><a href="https://mastodon.social/@katchwreck" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>katchwreck</span></a></span> For sure we won't understand how the brain works until the role of astrocytes and other glial cells is fully understood.<br>The <a href="https://mathstodon.xyz/tags/connectome" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>connectome</span></a> though is understood as the wiring diagram where neurons are nodes and edges are synaptic connections. For additional interactions there's the "<a href="https://mathstodon.xyz/tags/neuromodulome" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>neuromodulome</span></a>" for e.g., neuropeptide/neuromodulator vs. the corresponding receptor, like in this paper by Lidia Ripoll-Sánchez et al. 2023 on C. elegans: <br>"The neuropeptidergic connectome of C. elegans" <a href="https://www.cell.com/neuron/fulltext/S0896-6273(23)00756-0" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">cell.com/neuron/fulltext/S0896</span><span class="invisible">-6273(23)00756-0</span></a><br><a href="https://mathstodon.xyz/tags/neuroscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>neuroscience</span></a> <a href="https://mathstodon.xyz/tags/Celegans" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Celegans</span></a> <a href="https://mathstodon.xyz/tags/connectomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>connectomics</span></a></p>
katch wreck<p>i've seen a few papers in the last 10 years demonstrating direct <a href="https://mastodon.social/tags/astrocyte" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>astrocyte</span></a> involvement in a variety of brain functions normally associated with <a href="https://mastodon.social/tags/neurons" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>neurons</span></a>... does this mean that the definition of the <a href="https://mastodon.social/tags/connectome" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>connectome</span></a> should be somehow augmented with astrocyte topologies, relative to the neuronal ones?</p>
qurlyjoe<p>I was reading something the other day about new neurological research suggesting that while the <a href="https://mstdn.social/tags/connectome" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>connectome</span></a> is the physical foundation of the manifested mind, there may be another level manifested in the electrical fields generated by the synapses firing across the brain. And that’s where the mind lives, in the swirling fields. <a href="https://mstdn.social/tags/AI" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>AI</span></a> doesn’t have (yet) an equivalent physical foundation like ours, but when they do, we’re cooked.</p>
Maria Mannone<p><a href="https://fediscience.org/tags/Mathematical" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Mathematical</span></a> modeling of <a href="https://fediscience.org/tags/neurological" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>neurological</span></a> disease: what if we try to apply concepts and methods of <a href="https://fediscience.org/tags/theoretical" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>theoretical</span></a> <a href="https://fediscience.org/tags/physics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>physics</span></a> to <a href="https://fediscience.org/tags/medicine" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>medicine</span></a>? Maybe this could lead to new <a href="https://fediscience.org/tags/non" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>non</span></a>-invasive research methods. Enjoy!<br><a href="https://fediscience.org/tags/complexnetworks" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>complexnetworks</span></a> <a href="https://fediscience.org/tags/connectome" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>connectome</span></a> </p><p><a href="https://pubs.aip.org/aip/cha/article/34/5/053133/3294604/Modeling-a-neurological-disorder-as-the-result-of" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">pubs.aip.org/aip/cha/article/3</span><span class="invisible">4/5/053133/3294604/Modeling-a-neurological-disorder-as-the-result-of</span></a></p>
Gaspar Jekely<p>We 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">#<span>Platynereis</span></a> larval <a href="https://biologists.social/tags/connectome" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>connectome</span></a> with over 50 figures</p><p><a href="https://www.biorxiv.org/content/10.1101/2024.03.17.585258v1" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">biorxiv.org/content/10.1101/20</span><span class="invisible">24.03.17.585258v1</span></a></p><p>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">#<span>rstats</span></a> with the code provided:</p><p><a href="https://zenodo.org/doi/10.5281/zenodo.10825370" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">zenodo.org/doi/10.5281/zenodo.</span><span class="invisible">10825370</span></a></p><p><span class="h-card" translate="no"><a href="https://bird.makeup/users/zenodo_org" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>zenodo_org</span></a></span> </p><p>by querying our public <a href="https://biologists.social/tags/CATMAID" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CATMAID</span></a> database:</p><p><a href="https://catmaid.jekelylab.ex.ac.uk" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="">catmaid.jekelylab.ex.ac.uk</span><span class="invisible"></span></a></p><p><a href="https://biologists.social/tags/neuroscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>neuroscience</span></a> <span class="h-card" translate="no"><a href="https://mander.xyz/c/biology" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>biology</span></a></span> <a href="https://biologists.social/tags/volumeEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>volumeEM</span></a> <br><span class="h-card" translate="no"><a href="https://biologists.social/@biorxivpreprint" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>biorxivpreprint</span></a></span></p>
Meet Zandawala<p>Really excited to share the lab's first Drosophila paper and it's a big one. Check out our preprint <a href="https://shorturl.at/gqrvO" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="">shorturl.at/gqrvO</span><span class="invisible"></span></a> where we present the complete neural connectome of an animal circadian clock . 🧵 (1/8) <a href="https://drosophila.social/tags/Drosophila" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Drosophila</span></a> <a href="https://drosophila.social/tags/neuroscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>neuroscience</span></a> <a href="https://drosophila.social/tags/connectome" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>connectome</span></a></p>
Philip Hubbard<p>The <a href="https://fediscience.org/tags/HHMIJanelia" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>HHMIJanelia</span></a> FlyEM MANC <a href="https://fediscience.org/tags/connectome" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>connectome</span></a> is now available on NeuronBridge.janelia.org. <a href="https://fediscience.org/tags/Drosophila" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Drosophila</span></a> <a href="https://fediscience.org/tags/Neuroscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Neuroscience</span></a> researchers can use this tool to match the MANC electron <a href="https://fediscience.org/tags/microscopy" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>microscopy</span></a> (EM) data against light microscopy (LM) data, like that from the Janelia FlyLight project. A user can interactively examine matches right in the browser by clicking the "View in 3D" button. Interactive views are sharable, too... (1/3)</p>
Philip Hubbard<p>Today's <a href="https://fediscience.org/tags/neuroscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>neuroscience</span></a> news includes the release of the first fully-reconstructed <a href="https://fediscience.org/tags/connectome" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>connectome</span></a> for the ventral nerve cord (VNC) of the adult <a href="https://fediscience.org/tags/drosophila" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>drosophila</span></a>. This data set, known as the "MANC", is the result of collaboration between the FlyEM team at <a href="https://fediscience.org/tags/HHMIJanelia" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>HHMIJanelia</span></a> and teams from the University of <a href="https://fediscience.org/tags/Cambridge" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Cambridge</span></a> and <a href="https://fediscience.org/tags/Google" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Google</span></a> Research. (1/5)</p><p><a href="https://www.youtube.com/watch?v=0sKpSVZacyA" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">youtube.com/watch?v=0sKpSVZacy</span><span class="invisible">A</span></a></p>
Albert Cardona<p>Today the peer-reviewed version of our preprint is out:</p><p>"The <a href="https://mathstodon.xyz/tags/connectome" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>connectome</span></a> of an insect brain"<br><a href="https://www.science.org/doi/10.1126/science.add9330" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">science.org/doi/10.1126/scienc</span><span class="invisible">e.add9330</span></a></p><p>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.</p><p>See my <a href="https://mathstodon.xyz/tags/tootprint" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>tootprint</span></a> on the preprint from back in the Autumn: <a href="https://mathstodon.xyz/@albertcardona/109422190525090990" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">mathstodon.xyz/@albertcardona/</span><span class="invisible">109422190525090990</span></a></p><p>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">#<span>CATMAID</span></a> thanks to hosting by the <a href="https://mathstodon.xyz/tags/VirtualFlyBrain" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>VirtualFlyBrain</span></a>:<br><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"><span class="invisible">https://</span><span class="ellipsis">l1em.catmaid.virtualflybrain.o</span><span class="invisible">rg/?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</span></a>)</p><p>(The "Winding, Pedigo et al. 2023" annotation listing all included neurons will appear very soon in an upcoming update.)</p><p><a href="https://mathstodon.xyz/tags/neuroscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>neuroscience</span></a> <a href="https://mathstodon.xyz/tags/connectomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>connectomics</span></a> <a href="https://mathstodon.xyz/tags/Drosophila" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Drosophila</span></a> <a href="https://mathstodon.xyz/tags/DrosophilaLarva" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>DrosophilaLarva</span></a></p>
Albert Cardona<p>3,013 neurons, half a million synapses: the complete <a href="https://mathstodon.xyz/tags/connectome" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>connectome</span></a> of the whole <a href="https://mathstodon.xyz/tags/Drosophila" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Drosophila</span></a> larval brain!</p><p>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"><span class="invisible">https://www.</span><span class="ellipsis">biorxiv.org/content/10.1101/20</span><span class="invisible">22.11.28.516756v1</span></a></p><p>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/</p><p><a href="https://mathstodon.xyz/tags/neuroscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>neuroscience</span></a> <a href="https://mathstodon.xyz/tags/connectomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>connectomics</span></a> <a href="https://mathstodon.xyz/tags/vEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>vEM</span></a> <a href="https://mathstodon.xyz/tags/volumeEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>volumeEM</span></a></p>
Albert Cardona<p>The web-based open source software <a href="https://mathstodon.xyz/tags/CATMAID" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CATMAID</span></a> was devised as "google maps but for volumes". Documentation at <a href="https://catmaid.org" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="">catmaid.org</span><span class="invisible"></span></a> and source code at <a href="https://github.com/catmaid/CATMAID/" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="">github.com/catmaid/CATMAID/</span><span class="invisible"></span></a></p><p>Modern <a href="https://mathstodon.xyz/tags/CATMAID" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CATMAID</span></a> enables hundreds of <a href="https://mathstodon.xyz/tags/neuroscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>neuroscience</span></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">#<span>connectome</span></a>.</p><p>See the <a href="https://mathstodon.xyz/tags/Drosophila" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Drosophila</span></a> larval CNS at the <a href="https://mathstodon.xyz/tags/VirtualFlyBrain" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>VirtualFlyBrain</span></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"><span class="invisible">https://</span><span class="ellipsis">l1em.catmaid.virtualflybrain.o</span><span class="invisible">rg/?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</span></a>)</p>
Albert Cardona<p><a href="https://mathstodon.xyz/tags/introduction" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>introduction</span></a> To fill in my profile tags, a thread:</p><p><a href="https://mathstodon.xyz/tags/TrakEM2" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>TrakEM2</span></a> open source software mostly for <a href="https://mathstodon.xyz/tags/connectomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>connectomics</span></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">#<span>SIFT</span></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">#<span>connectome</span></a> from <a href="https://mathstodon.xyz/tags/vEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>vEM</span></a> (volume electron microscopy).</p><p>See: <a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0038011" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">journals.plos.org/plosone/arti</span><span class="invisible">cle?id=10.1371/journal.pone.0038011</span></a></p><p>Git repository at: <a href="https://github.com/trakem2/" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="">github.com/trakem2/</span><span class="invisible"></span></a></p>
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