Albert Cardona<p>Sometimes one stops to just look at the data. And the software user interface. They are beautiful.</p><p>We are looking at a cross section of the <a href="https://mathstodon.xyz/tags/Drosophila" class="mention hashtag" rel="tag">#<span>Drosophila</span></a> larval brain, near the brain commissure, where hundreds of neurons (magenta: their reconstructed skeletons) cross from one brain hemisphere to the other. To the right, a 3D rendering of multiple neurons, a pair of which cross the midline in a U-shaped bend.</p><p>Our CATMAID software is web-based, in other words it's just a website that accesses remote data. I credit it's sleek design to <span class="h-card" translate="no"><a href="https://mastodon.social/@herrsaalfeld" class="u-url mention">@<span>herrsaalfeld</span></a></span> – author of the early, "Ice Age" CATMAID and its blue tones – who at some point in his life studied "medieninformatik" and has always had a penchant for art.</p><p>See our images and fly neurons here, kindly hosted 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=33100&yp=31179&xp=53333&tool=tracingtool&sid0=1&s0=2" 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=33100&yp=31179&xp=53333&tool=tracingtool&sid0=1&s0=2</span></a></p><p><a href="https://mathstodon.xyz/tags/neuroscience" class="mention hashtag" rel="tag">#<span>neuroscience</span></a> <a href="https://mathstodon.xyz/tags/CATMAID" class="mention hashtag" rel="tag">#<span>CATMAID</span></a></p>
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dancwart<p>Merry Pancakemas, and happy last Pancake Thursday of the year!</p><p><a href="https://mastodon.art/tags/christmas" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>christmas</span></a> <a href="https://mastodon.art/tags/christmas2024" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>christmas2024</span></a> <a href="https://mastodon.art/tags/pancakethursday" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>pancakethursday</span></a> <a href="https://mastodon.art/tags/pancakes" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>pancakes</span></a> <a href="https://mastodon.art/tags/cat" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>cat</span></a> <a href="https://mastodon.art/tags/kemonomimi" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>kemonomimi</span></a> <a href="https://mastodon.art/tags/catmaid" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>catmaid</span></a> <a href="https://mastodon.art/tags/maid" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>maid</span></a> <a href="https://mastodon.art/tags/originalcharacter" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>originalcharacter</span></a> <a href="https://mastodon.art/tags/art" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>art</span></a> <a href="https://mastodon.art/tags/MastoArt" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>MastoArt</span></a></p>
Teixi<p><span class="h-card" translate="no"><a href="https://qoto.org/@uni_matrix" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>uni_matrix</span></a></span> <span class="h-card" translate="no"><a href="https://qoto.org/@davi" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>davi</span></a></span> </p><p>ps: also includes nice paragraph on <a href="https://mastodon.social/tags/TrakEM2" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>TrakEM2</span></a> by <span class="h-card" translate="no"><a href="https://mathstodon.xyz/@albertcardona" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>albertcardona</span></a></span> et al. w/ remark on alignments errors auto correction.</p><p>As for <a href="https://mastodon.social/tags/catmaid" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>catmaid</span></a> collaborative annotation & neuronal structures skeletons approach!</p>
Albert Cardona<p><span class="h-card" translate="no"><a href="https://mstdn.science/@CurrentBiology" class="u-url mention">@<span>CurrentBiology</span></a></span> </p><p>Andreas Schoofs and Anton Miroschnikow in Michael Pankratz' lab have done an astonishing amount of work manually mapping the peripheral nervous system of the larval <a href="https://mathstodon.xyz/tags/Drosophila" class="mention hashtag" rel="tag">#<span>Drosophila</span></a>, with <a href="https://mathstodon.xyz/tags/CATMAID" class="mention hashtag" rel="tag">#<span>CATMAID</span></a>, in the STEM volume we imaged and they named "Igor". Congrats on seeing this gargantuan project through!</p><p>The whole larval volume of "Igor", including all tissues, is available here, courtesy of the <a href="https://mathstodon.xyz/tags/OpenOrganelle" class="mention hashtag" rel="tag">#<span>OpenOrganelle</span></a> project led by Aubrey Weigel <span class="h-card" translate="no"><a href="https://qoto.org/@avweigel" class="u-url mention">@<span>avweigel</span></a></span> at <a href="https://mathstodon.xyz/tags/HHMIJanelia" class="mention hashtag" rel="tag">#<span>HHMIJanelia</span></a>:<br /><a href="https://openorganelle.janelia.org/datasets/jrc_fly-larva-1" target="_blank" rel="nofollow noopener noreferrer" translate="no"><span class="invisible">https://</span><span class="ellipsis">openorganelle.janelia.org/data</span><span class="invisible">sets/jrc_fly-larva-1</span></a></p><p>See it at 5x5x35 nm resolution in <a href="https://mathstodon.xyz/tags/neuroglancer" class="mention hashtag" rel="tag">#<span>neuroglancer</span></a>: <a href="https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22:%7B%22x%22:%5B1e-9%2C%22m%22%5D%2C%22y%22:%5B1e-9%2C%22m%22%5D%2C%22z%22:%5B1e-9%2C%22m%22%5D%7D%2C%22position%22:%5B249600.5%2C79040.5%2C84280.5%5D%2C%22crossSectionOrientation%22:%5B0%2C1%2C0%2C0%5D%2C%22crossSectionScale%22:50%2C%22projectionOrientation%22:%5B0%2C1%2C0%2C0%5D%2C%22projectionScale%22:65536%2C%22layers%22:%5B%7B%22type%22:%22image%22%2C%22source%22:%22n5://s3://janelia-cosem-datasets/jrc_fly-larva-1/jrc_fly-larva-1.n5/em/tem-uint8%22%2C%22tab%22:%22rendering%22%2C%22opacity%22:1%2C%22blend%22:%22additive%22%2C%22shader%22:%22#uicontrol%20invlerp%20normalized%28range=%5B0%2C%20255%5D%2C%20window=%5B0%2C%20255%5D%29%5Cn#uicontrol%20vec3%20color%20color%28default=%5C%22white%5C%22%29%5Cnvoid%20main%28%29%7BemitRGB%28color%20%2A%20normalized%28%29%29%3B%7D%22%2C%22name%22:%22tem-uint8%22%7D%5D%2C%22selectedLayer%22:%7B%22visible%22:true%2C%22layer%22:%22tem-uint8%22%7D%2C%22crossSectionBackgroundColor%22:%22#000000%22%2C%22layout%22:%224panel%22%7D" target="_blank" rel="nofollow noopener noreferrer" translate="no"><span class="invisible">https://</span><span class="ellipsis">neuroglancer-demo.appspot.com/</span><span class="invisible">#!%7B%22dimensions%22:%7B%22x%22:%5B1e-9%2C%22m%22%5D%2C%22y%22:%5B1e-9%2C%22m%22%5D%2C%22z%22:%5B1e-9%2C%22m%22%5D%7D%2C%22position%22:%5B249600.5%2C79040.5%2C84280.5%5D%2C%22crossSectionOrientation%22:%5B0%2C1%2C0%2C0%5D%2C%22crossSectionScale%22:50%2C%22projectionOrientation%22:%5B0%2C1%2C0%2C0%5D%2C%22projectionScale%22:65536%2C%22layers%22:%5B%7B%22type%22:%22image%22%2C%22source%22:%22n5://s3://janelia-cosem-datasets/jrc_fly-larva-1/jrc_fly-larva-1.n5/em/tem-uint8%22%2C%22tab%22:%22rendering%22%2C%22opacity%22:1%2C%22blend%22:%22additive%22%2C%22shader%22:%22#uicontrol%20invlerp%20normalized%28range=%5B0%2C%20255%5D%2C%20window=%5B0%2C%20255%5D%29%5Cn#uicontrol%20vec3%20color%20color%28default=%5C%22white%5C%22%29%5Cnvoid%20main%28%29%7BemitRGB%28color%20%2A%20normalized%28%29%29%3B%7D%22%2C%22name%22:%22tem-uint8%22%7D%5D%2C%22selectedLayer%22:%7B%22visible%22:true%2C%22layer%22:%22tem-uint8%22%7D%2C%22crossSectionBackgroundColor%22:%22#000000%22%2C%22layout%22:%224panel%22%7D</span></a> (control-minus and control-plus to zoom; mouse click to pan, scroll wheel to browse in Z).</p><p>Will appear at the <a href="https://mathstodon.xyz/tags/VirtualFlyBrain" class="mention hashtag" rel="tag">#<span>VirtualFlyBrain</span></a> website soon as well.</p><p>There are many more peripheral nervous system components mapped, yet to be published.</p><p>This paper is open access: <br />"Serotonergic modulation of swallowing in a complete fly vagus nerve connectome", Schoofs et al. 2024 <a href="https://www.cell.com/current-biology/fulltext/S0960-9822(24)01137-0?rss=yes&utm_source=dlvr.it&utm_medium=mastodon" target="_blank" rel="nofollow noopener noreferrer" translate="no"><span class="invisible">https://www.</span><span class="ellipsis">cell.com/current-biology/fullt</span><span class="invisible">ext/S0960-9822(24)01137-0?rss=yes&utm_source=dlvr.it&utm_medium=mastodon</span></a></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></p>
dancwart<p>"May I take your order, dear customer... I highly recommend the pancakes"</p><p><a href="https://mastodon.art/tags/jojosbizarreadventure" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>jojosbizarreadventure</span></a> <a href="https://mastodon.art/tags/jba" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>jba</span></a> <a href="https://mastodon.art/tags/parody" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>parody</span></a> <a href="https://mastodon.art/tags/OriginalCharacter" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>OriginalCharacter</span></a> <a href="https://mastodon.art/tags/catmaid" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>catmaid</span></a> <a href="https://mastodon.art/tags/art" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>art</span></a> <a href="https://mastodon.art/tags/MastoArt" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>MastoArt</span></a></p>
Albert Cardona<p><span class="h-card" translate="no"><a href="https://mastodon.social/@Raf" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>Raf</span></a></span> </p><p>El PostGIS funciona de meravella. Fa anys i panys que el fem servir per a la base de dades de <a href="https://mastodont.cat/tags/CATMAID" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CATMAID</span></a>, el nostre programari lliure per a mapar neurones en volums de sistemes nerviosos:<br><a href="https://catmaid.readthedocs.io/" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="">catmaid.readthedocs.io/</span><span class="invisible"></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>
Albert Cardona<p><span class="h-card" translate="no"><a href="https://neuromatch.social/@adredish" class="u-url mention">@<span>adredish</span></a></span> <span class="h-card" translate="no"><a href="https://neuromatch.social/@neuralreckoning" class="u-url mention">@<span>neuralreckoning</span></a></span> <span class="h-card" translate="no"><a href="https://mastodon.social/@brembs" class="u-url mention">@<span>brembs</span></a></span> <span class="h-card" translate="no"><a href="https://neuromatch.social/@ScholarNexus" class="u-url mention">@<span>ScholarNexus</span></a></span> </p><p>Likewise for <a href="https://mathstodon.xyz/tags/TrakEM2" class="mention hashtag" rel="tag">#<span>TrakEM2</span></a>, <a href="https://mathstodon.xyz/tags/FijiSc" class="mention hashtag" rel="tag">#<span>FijiSc</span></a> and <a href="https://mathstodon.xyz/tags/catmaid" class="mention hashtag" rel="tag">#<span>catmaid</span></a> software – except we did write papers for them.</p>
dancwart<p>Happy Pancake Thursday!</p><p>I've learned that Hellboy likes cats, too, so here's a follow-up of last weeks post.</p><p><a href="https://mastodon.art/tags/hellboy" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>hellboy</span></a> <a href="https://mastodon.art/tags/PancakeThursday" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>PancakeThursday</span></a> <a href="https://mastodon.art/tags/cats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>cats</span></a> <a href="https://mastodon.art/tags/CatMaid" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CatMaid</span></a> <a href="https://mastodon.art/tags/MaidOutfit" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>MaidOutfit</span></a> <a href="https://mastodon.art/tags/catboy" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>catboy</span></a> <a href="https://mastodon.art/tags/catgirl" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>catgirl</span></a> <a href="https://mastodon.art/tags/catcaf%C3%A9" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>catcafé</span></a> <a href="https://mastodon.art/tags/cafe" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>cafe</span></a> <a href="https://mastodon.art/tags/pancakes" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>pancakes</span></a> <a href="https://mastodon.art/tags/myart" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>myart</span></a> <a href="https://mastodon.art/tags/art" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>art</span></a> <a href="https://mastodon.art/tags/MastoArt" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>MastoArt</span></a></p>
Albert Cardona<p>A connectome of the optic lobe of the extremely tiny fairy wasp, Megaphragma sp.</p><p>"A complete reconstruction of the early visual system of an adult insect", by Chua et al. 2023 (Chklovskii & Polilov) <a href="https://www.sciencedirect.com/science/article/pii/S096098222301237X" target="_blank" rel="nofollow noopener noreferrer" translate="no"><span class="invisible">https://www.</span><span class="ellipsis">sciencedirect.com/science/arti</span><span class="invisible">cle/pii/S096098222301237X</span></a></p><p>Don't miss the supplemental figures.</p><p>"Compared with the honeybee and the fruit fly, Megaphragma exhibits the following miniaturization-related adaptations: a significant reduction in the number of ommatidia, absence of several cell types, reduced size, and denucleation of neurons. Interestingly, the reduction in lens diameter is less than that expected from the optimization of the optical resolution of the eye. This suggests that light sensitivity is a more important<br />consideration when lens diameter approaches the wavelength of light. The absence of wide-field (or non-columnar) lamina neurons in Megaphragma could be a consequence of the smaller number of ommatidia, their larger acceptance angle, and the lower resolving power of the eye."</p><p>Volume assembled with <a href="https://mathstodon.xyz/tags/FijiSc" class="mention hashtag" rel="tag">#<span>FijiSc</span></a> and <a href="https://mathstodon.xyz/tags/TrakEM2" class="mention hashtag" rel="tag">#<span>TrakEM2</span></a>, and its neurons and synapses mapped with <a href="https://mathstodon.xyz/tags/CATMAID" class="mention hashtag" rel="tag">#<span>CATMAID</span></a>. Woohoo!</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/VolumeEM" class="mention hashtag" rel="tag">#<span>VolumeEM</span></a> <a href="https://mathstodon.xyz/tags/vEM" class="mention hashtag" rel="tag">#<span>vEM</span></a> <a href="https://mathstodon.xyz/tags/insects" class="mention hashtag" rel="tag">#<span>insects</span></a> <a href="https://mathstodon.xyz/tags/miniaturization" class="mention hashtag" rel="tag">#<span>miniaturization</span></a></p>
Albert Cardona<p>Avui ha sortit publicada la versió avaluada per experts del nostre article descrivint el <a href="https://mastodont.cat/tags/connectoma" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>connectoma</span></a> [1] del cervell de la larva de la mosca del vinagre. Unes 3,000 neurones i més de mig milió de sinàpsis, traçades a mà amb el nostre programmari especialitzat i de codi obert, <a href="https://mastodont.cat/tags/Catmaid" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Catmaid</span></a>. En anglès, aquí:</p><p>"The connectome of an insect brain"<br><a href="https://www.science.org/doi/10.1126/science.add9330" rel="nofollow noopener noreferrer" 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><a href="https://mastodont.cat/tags/Vilaweb" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Vilaweb</span></a> se n'ha fet ressò: <a href="https://www.vilaweb.cat/noticies/cervell-neurona-neurona-investigacio-deu-anys-crea-mapa-mes-complex-mai-fet/" rel="nofollow noopener noreferrer" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">vilaweb.cat/noticies/cervell-n</span><span class="invisible">eurona-neurona-investigacio-deu-anys-crea-mapa-mes-complex-mai-fet/</span></a></p><p><a href="https://mastodont.cat/tags/neurobiologia" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>neurobiologia</span></a> <a href="https://mastodont.cat/tags/CadaDiaCi%C3%A8ncia" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CadaDiaCiència</span></a> <a href="https://mastodont.cat/tags/ci%C3%A8ncia" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>ciència</span></a></p><p>[1] <a href="https://ca.wikipedia.org/wiki/Connectoma" rel="nofollow noopener noreferrer" target="_blank"><span class="invisible">https://</span><span class="ellipsis">ca.wikipedia.org/wiki/Connecto</span><span class="invisible">ma</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="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>
Gaspar Jekely<p>In this paper we generated most of the figures entirely in R for open science and reproducibility. All code is shared here:<br><a href="https://github.com/JekelyLab/Jasek_et_al" rel="nofollow noopener noreferrer" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/JekelyLab/Jasek_et_</span><span class="invisible">al</span></a><br>The figures and analyses can be regenerated by the code that will query our public <a href="https://qoto.org/tags/CATMAID" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CATMAID</span></a> database where all EM data, tracings and annotations are shared:<br><a href="https://catmaid.jekelylab.ex.ac.uk" rel="nofollow noopener noreferrer" target="_blank"><span class="invisible">https://</span><span class="">catmaid.jekelylab.ex.ac.uk</span><span class="invisible"></span></a> (project id: 11)<br><a href="https://qoto.org/tags/openscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>openscience</span></a> <a href="https://qoto.org/tags/rstat" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>rstat</span></a></p>
Albert Cardona<p><span class="h-card" translate="no"><a href="https://drosophila.social/@dantracey" class="u-url mention">@<span>dantracey</span></a></span> <span class="h-card" translate="no"><a href="https://social.coop/@kristinmbranson" class="u-url mention">@<span>kristinmbranson</span></a></span> <span class="h-card" translate="no"><a href="https://drosophila.social/@annikabarber" class="u-url mention">@<span>annikabarber</span></a></span> <span class="h-card" translate="no"><a href="https://drosophila.social/@debivort" class="u-url mention">@<span>debivort</span></a></span> <span class="h-card" translate="no"><a href="https://drosophila.social/@giorgiogilestro" class="u-url mention">@<span>giorgiogilestro</span></a></span></p><p>Find the original basin-1 neurons at the <a href="https://mathstodon.xyz/tags/VirtualFlyBrain" class="mention hashtag" rel="tag">#<span>VirtualFlyBrain</span></a> at "Tools - CATMAID - Hosted EM Data - Larval - Larva (ABD1.5)" which opens a <a href="https://mathstodon.xyz/tags/CATMAID" class="mention hashtag" rel="tag">#<span>CATMAID</span></a> server <a href="https://abd1.5.catmaid.virtualflybrain.org/?pid=1&zp=10485&yp=40560.65722061269&xp=42396.0789533435&tool=tracingtool&sid0=1&s0=4.5&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">abd1.5.catmaid.virtualflybrain</span><span class="invisible">.org/?pid=1&zp=10485&yp=40560.65722061269&xp=42396.0789533435&tool=tracingtool&sid0=1&s0=4.5&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>Find them via Neuron Search (icon with a "?").</p><p>The "Construction time" is wrong (see "Summary info" of the Selection Table) because these neurons were imported from <a href="https://mathstodon.xyz/tags/TrakEM2" class="mention hashtag" rel="tag">#<span>TrakEM2</span></a>. Old enough to predate the <a href="https://mathstodon.xyz/tags/CATMAID" class="mention hashtag" rel="tag">#<span>CATMAID</span></a> software!<br /><a href="https://mathstodon.xyz/tags/neuroscience" class="mention hashtag" rel="tag">#<span>neuroscience</span></a></p>
Albert Cardona<p>Quite pleased with our preprint on the <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, as reconstructed with <a href="https://mathstodon.xyz/tags/CATMAID" class="mention hashtag" rel="tag">#<span>CATMAID</span></a> from <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> and analysed from a graph-theoretic perspective.</p><p>The bioRxiv lists ~10,000 abstract views and nearly ~2,000 PDF downloads over two weeks. Thanks so much everyone for your interest in our research!</p><p>Preprint: <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>See original <a href="https://mathstodon.xyz/tags/tootorial" class="mention hashtag" rel="tag">#<span>tootorial</span></a> thread:<br /><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>
Albert Cardona<p><span class="h-card" translate="no"><a href="https://drosophila.social/@Gontijo" class="u-url mention">@<span>Gontijo</span></a></span> Thanks! And very good question: I'm preparing a guide everyone on finding their favourite <a href="https://mathstodon.xyz/tags/Drosophila" class="mention hashtag" rel="tag">#<span>Drosophila</span></a> larval neurons in <a href="https://mathstodon.xyz/tags/CATMAID" class="mention hashtag" rel="tag">#<span>CATMAID</span></a>.</p><p>1st, all neurons will appear in the VirtualFlyBrain website soonish. We have to send in an update with all neurons newly added in this paper.</p><p>2nd, there are tools from <span class="h-card" translate="no"><a href="https://drosophila.social/@drosofriend" class="u-url mention">@<span>drosofriend</span></a></span>'s and Douglas Armstrong's lab for NBLASTing James W. Truman catalogue of LSM images of GAL4 lines (GMR and Vienna tiles) against EM-reconstructed neurons.</p><p>All in due time :)</p>
Albert Cardona<p><span class="h-card" translate="no"><a href="https://mastodon.me.uk/@mhl20" class="u-url mention">@<span>mhl20</span></a></span> Thanks Marc! <a href="https://mathstodon.xyz/tags/CATMAID" class="mention hashtag" rel="tag">#<span>CATMAID</span></a> lists ~8,000 hours of reconstruction work and ~3,000 hours of proofreading work to complete the whole <a href="https://mathstodon.xyz/tags/Drosophila" class="mention hashtag" rel="tag">#<span>Drosophila</span></a> larval brain <a href="https://mathstodon.xyz/tags/connectome" class="mention hashtag" rel="tag">#<span>connectome</span></a>. And as you know this is likely an underestimate.</p>
Albert Cardona<p>A huge THANK YOU to everyone that worked on this project for 10 years, starting with first co-authors Michael Winding and Ben Pedigo at University of Cambridge and Johns Hopkins. A collaboration with Marta Zlatic, Carey E. Priebe, and Joshua Vogelstein.</p><p>This work started at <a href="https://mathstodon.xyz/tags/HHMIJanelia" class="mention hashtag" rel="tag">#<span>HHMIJanelia</span></a> and continued at the <a href="https://mathstodon.xyz/tags/MRCLMB" class="mention hashtag" rel="tag">#<span>MRCLMB</span></a> in Cambridge, UK.</p><p>All neuron reconstructions were done painstakingly by hand with <a href="https://mathstodon.xyz/tags/CATMAID" class="mention hashtag" rel="tag">#<span>CATMAID</span></a> by over >80 people! Thanks so much!</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><br />/END</p>
Albert Cardona<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>
Albert Cardona<p><a href="https://mathstodon.xyz/tags/TrakEM2" class="mention hashtag" rel="tag">#<span>TrakEM2</span></a> runs as a plugin of <a href="https://mathstodon.xyz/tags/FijiSc" class="mention hashtag" rel="tag">#<span>FijiSc</span></a> <a href="https://fiji.sc/" target="_blank" rel="nofollow noopener noreferrer" translate="no"><span class="invisible">https://</span><span class="">fiji.sc/</span><span class="invisible"></span></a> and in fact motivated the creation of the <a href="https://mathstodon.xyz/tags/FijiSc" class="mention hashtag" rel="tag">#<span>FijiSc</span></a> software in the first place, to manage its many dependencies and facilitate distribution to the broader <a href="https://mathstodon.xyz/tags/neuroscience" class="mention hashtag" rel="tag">#<span>neuroscience</span></a> community.</p><p><a href="https://mathstodon.xyz/tags/TrakEM2" class="mention hashtag" rel="tag">#<span>TrakEM2</span></a> was founded in 2005, when TB-sized datasets were rare and considered large. Largest dataset I've successfully managed with <a href="https://mathstodon.xyz/tags/TrakEM2" class="mention hashtag" rel="tag">#<span>TrakEM2</span></a> was ~16 TB. For larger volumes see <a href="https://mathstodon.xyz/tags/CATMAID" class="mention hashtag" rel="tag">#<span>CATMAID</span></a>.</p><p>For 3D visualization <a href="https://mathstodon.xyz/tags/TrakEM2" class="mention hashtag" rel="tag">#<span>TrakEM2</span></a> uses the 3D Viewer <a href="https://imagej.net/plugins/3d-viewer/" target="_blank" rel="nofollow noopener noreferrer" translate="no"><span class="invisible">https://</span><span class="">imagej.net/plugins/3d-viewer/</span><span class="invisible"></span></a></p>
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