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"content": "<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=\"tag\">#<span>connectome</span></a> of an insect brain"<br /><a href=\"https://www.science.org/doi/10.1126/science.add9330\" target=\"_blank\" rel=\"nofollow noopener noreferrer\" translate=\"no\"><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=\"tag\">#<span>tootprint</span></a> on the preprint from back in the Autumn: <a href=\"https://mathstodon.xyz/@albertcardona/109422190525090990\" target=\"_blank\" rel=\"nofollow noopener noreferrer\" translate=\"no\"><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=\"tag\">#<span>CATMAID</span></a> thanks to hosting by the <a href=\"https://mathstodon.xyz/tags/VirtualFlyBrain\" class=\"mention hashtag\" rel=\"tag\">#<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\" target=\"_blank\" rel=\"nofollow noopener noreferrer\" translate=\"no\"><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=\"tag\">#<span>neuroscience</span></a> <a href=\"https://mathstodon.xyz/tags/connectomics\" class=\"mention hashtag\" rel=\"tag\">#<span>connectomics</span></a> <a href=\"https://mathstodon.xyz/tags/Drosophila\" class=\"mention hashtag\" rel=\"tag\">#<span>Drosophila</span></a> <a href=\"https://mathstodon.xyz/tags/DrosophilaLarva\" class=\"mention hashtag\" rel=\"tag\">#<span>DrosophilaLarva</span></a></p>",
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"en": "<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=\"tag\">#<span>connectome</span></a> of an insect brain"<br /><a href=\"https://www.science.org/doi/10.1126/science.add9330\" target=\"_blank\" rel=\"nofollow noopener noreferrer\" translate=\"no\"><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=\"tag\">#<span>tootprint</span></a> on the preprint from back in the Autumn: <a href=\"https://mathstodon.xyz/@albertcardona/109422190525090990\" target=\"_blank\" rel=\"nofollow noopener noreferrer\" translate=\"no\"><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=\"tag\">#<span>CATMAID</span></a> thanks to hosting by the <a href=\"https://mathstodon.xyz/tags/VirtualFlyBrain\" class=\"mention hashtag\" rel=\"tag\">#<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\" target=\"_blank\" rel=\"nofollow noopener noreferrer\" translate=\"no\"><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=\"tag\">#<span>neuroscience</span></a> <a href=\"https://mathstodon.xyz/tags/connectomics\" class=\"mention hashtag\" rel=\"tag\">#<span>connectomics</span></a> <a href=\"https://mathstodon.xyz/tags/Drosophila\" class=\"mention hashtag\" rel=\"tag\">#<span>Drosophila</span></a> <a href=\"https://mathstodon.xyz/tags/DrosophilaLarva\" class=\"mention hashtag\" rel=\"tag\">#<span>DrosophilaLarva</span></a></p>"
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"content": "<p>3,013 neurons, half a million synapses: the complete <a href=\"https://mathstodon.xyz/tags/connectome\" class=\"mention hashtag\" rel=\"tag\">#<span>connectome</span></a> of the whole <a href=\"https://mathstodon.xyz/tags/Drosophila\" class=\"mention hashtag\" rel=\"tag\">#<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\" target=\"_blank\" rel=\"nofollow noopener noreferrer\" translate=\"no\"><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=\"tag\">#<span>neuroscience</span></a> <a href=\"https://mathstodon.xyz/tags/connectomics\" class=\"mention hashtag\" rel=\"tag\">#<span>connectomics</span></a> <a href=\"https://mathstodon.xyz/tags/vEM\" class=\"mention hashtag\" rel=\"tag\">#<span>vEM</span></a> <a href=\"https://mathstodon.xyz/tags/volumeEM\" class=\"mention hashtag\" rel=\"tag\">#<span>volumeEM</span></a></p>",
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"content": "<p><a href=\"https://mathstodon.xyz/tags/introduction\" class=\"mention hashtag\" rel=\"tag\">#<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=\"tag\">#<span>TrakEM2</span></a> open source software mostly for <a href=\"https://mathstodon.xyz/tags/connectomics\" class=\"mention hashtag\" rel=\"tag\">#<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=\"tag\">#<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=\"tag\">#<span>connectome</span></a> from <a href=\"https://mathstodon.xyz/tags/vEM\" class=\"mention hashtag\" rel=\"tag\">#<span>vEM</span></a> (volume electron microscopy).</p><p>See: <a href=\"https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0038011\" target=\"_blank\" rel=\"nofollow noopener noreferrer\" translate=\"no\"><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/\" target=\"_blank\" rel=\"nofollow noopener noreferrer\" translate=\"no\"><span class=\"invisible\">https://</span><span class=\"\">github.com/trakem2/</span><span class=\"invisible\"></span></a></p>",
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"content": "<p>The web-based open source software <a href=\"https://mathstodon.xyz/tags/CATMAID\" class=\"mention hashtag\" rel=\"tag\">#<span>CATMAID</span></a> was devised as "google maps but for volumes". Documentation at <a href=\"https://catmaid.org\" target=\"_blank\" rel=\"nofollow noopener noreferrer\" translate=\"no\"><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/\" target=\"_blank\" rel=\"nofollow noopener noreferrer\" translate=\"no\"><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=\"tag\">#<span>CATMAID</span></a> enables hundreds of <a href=\"https://mathstodon.xyz/tags/neuroscience\" class=\"mention hashtag\" rel=\"tag\">#<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=\"tag\">#<span>connectome</span></a>.</p><p>See the <a href=\"https://mathstodon.xyz/tags/Drosophila\" class=\"mention hashtag\" rel=\"tag\">#<span>Drosophila</span></a> larval CNS at the <a href=\"https://mathstodon.xyz/tags/VirtualFlyBrain\" class=\"mention hashtag\" rel=\"tag\">#<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\" target=\"_blank\" rel=\"nofollow noopener noreferrer\" translate=\"no\"><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>",
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"en": "<p>The web-based open source software <a href=\"https://mathstodon.xyz/tags/CATMAID\" class=\"mention hashtag\" rel=\"tag\">#<span>CATMAID</span></a> was devised as "google maps but for volumes". Documentation at <a href=\"https://catmaid.org\" target=\"_blank\" rel=\"nofollow noopener noreferrer\" translate=\"no\"><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/\" target=\"_blank\" rel=\"nofollow noopener noreferrer\" translate=\"no\"><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=\"tag\">#<span>CATMAID</span></a> enables hundreds of <a href=\"https://mathstodon.xyz/tags/neuroscience\" class=\"mention hashtag\" rel=\"tag\">#<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=\"tag\">#<span>connectome</span></a>.</p><p>See the <a href=\"https://mathstodon.xyz/tags/Drosophila\" class=\"mention hashtag\" rel=\"tag\">#<span>Drosophila</span></a> larval CNS at the <a href=\"https://mathstodon.xyz/tags/VirtualFlyBrain\" class=\"mention hashtag\" rel=\"tag\">#<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\" target=\"_blank\" rel=\"nofollow noopener noreferrer\" translate=\"no\"><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>"
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