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="nofollow noopener noreferrer" target="_blank">#<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" rel="nofollow noopener noreferrer" target="_blank">@<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="nofollow noopener noreferrer" target="_blank">#<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" 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=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="nofollow noopener noreferrer" target="_blank">#<span>neuroscience</span></a> <a href="https://mathstodon.xyz/tags/CATMAID" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CATMAID</span></a></p>
Recent searches
No recent searches
Search options
Only available when logged in.
social.tchncs.de is one of the many independent Mastodon servers you can use to participate in the fediverse.
A friendly server from Germany – which tends to attract techy people, but welcomes everybody. This is one of the oldest Mastodon instances.
Administered by:
Server stats:
3.8Kactive users
social.tchncs.de: About · Profiles directory · Privacy policy
Mastodon: About · Get the app · Keyboard shortcuts · View source code · v4.3.7
#VirtualFlyBrain
0 posts · 0 participants · 0 posts today
Albert Cardona<p><span class="h-card" translate="no"><a href="https://mstdn.science/@CurrentBiology" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<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="nofollow noopener noreferrer" target="_blank">#<span>Drosophila</span></a>, with <a href="https://mathstodon.xyz/tags/CATMAID" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<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="nofollow noopener noreferrer" target="_blank">#<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" rel="nofollow noopener noreferrer" target="_blank">@<span>avweigel</span></a></span> at <a href="https://mathstodon.xyz/tags/HHMIJanelia" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>HHMIJanelia</span></a>:<br><a href="https://openorganelle.janelia.org/datasets/jrc_fly-larva-1" rel="nofollow noopener noreferrer" translate="no" target="_blank"><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="nofollow noopener noreferrer" target="_blank">#<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" rel="nofollow noopener noreferrer" translate="no" target="_blank"><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="nofollow noopener noreferrer" target="_blank">#<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" rel="nofollow noopener noreferrer" translate="no" target="_blank"><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="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></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" 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" 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" 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><span class="h-card"><a href="https://drosophila.social/@dantracey" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>dantracey</span></a></span> <span class="h-card"><a href="https://social.coop/@kristinmbranson" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>kristinmbranson</span></a></span> <span class="h-card"><a href="https://drosophila.social/@annikabarber" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>annikabarber</span></a></span> <span class="h-card"><a href="https://drosophila.social/@debivort" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>debivort</span></a></span> <span class="h-card"><a href="https://drosophila.social/@giorgiogilestro" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<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="nofollow noopener noreferrer" target="_blank">#<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="nofollow noopener noreferrer" target="_blank">#<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" rel="nofollow noopener noreferrer" target="_blank"><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="nofollow noopener noreferrer" target="_blank">#<span>TrakEM2</span></a>. Old enough to predate the <a href="https://mathstodon.xyz/tags/CATMAID" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CATMAID</span></a> software!<br><a href="https://mathstodon.xyz/tags/neuroscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>neuroscience</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" 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" 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" 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>Have you visited the <a href="https://qoto.org/tags/FlyWire" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>FlyWire</span></a> website yet? Both for helping proofread and analyze the whole <a href="https://qoto.org/tags/Drosophila" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Drosophila</span></a> brain <a href="https://qoto.org/tags/connectome" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>connectome</span></a>, or simply to admire the beautiful renderings of neuronal arbors: <a href="https://join.flywire.ai" rel="nofollow noopener noreferrer" target="_blank"><span class="invisible">https://</span><span class="">join.flywire.ai</span><span class="invisible"></span></a></p><p>(See also the <a href="https://qoto.org/tags/VirtualFlyBrain" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>VirtualFlyBrain</span></a> for <a href="https://qoto.org/tags/ontology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>ontology</span></a>-driven navigation of the fly brain, and access to images of genetic driver lines, and more: <a href="https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?id=VFB_00101567&i=VFB_00101567" rel="nofollow noopener noreferrer" target="_blank"><span class="invisible">https://</span><span class="ellipsis">v2.virtualflybrain.org/org.gep</span><span class="invisible">petto.frontend/geppetto?id=VFB_00101567&i=VFB_00101567</span></a> )</p><p>Wish I had time or resources to create such a beautiful landing page for the larval central nervous system. The <a href="https://qoto.org/tags/connectome" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>connectome</span></a> of the whole larval brain is coming soon. For now, see the <a href="https://qoto.org/tags/vEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>vEM</span></a> images and some ~3,000 published neurons in this <a href="https://qoto.org/tags/CATMAID" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CATMAID</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" 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><a href="https://qoto.org/tags/connectomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>connectomics</span></a></p>
Albert Cardona<p>What can you do with a <a href="https://qoto.org/tags/CATMAID" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CATMAID</span></a> server? Say, let's look at the <a href="https://qoto.org/tags/Drosophila" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Drosophila</span></a> (vinegar fly, often referred to as fruit fly) larval central nervous system, generously hosted by the <a href="https://qoto.org/tags/VirtualFlyBrain" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>VirtualFlyBrain</span></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" 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>) or the <a href="https://qoto.org/tags/Platynereis" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Platynereis</span></a> (a marine annelid) server from the Jekely lab <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></p><p>First, directly interact by point-and-click: open widgets, find neurons by name or annotations, fire up a graph widget and rearrange neurons to make a neat synaptic connectivity diagram, or an adjacency matrix, or look at neuron anatomy in 3D. Most text–names, numbers–are clickable and filterable in some way, such as regular expressions.</p><p>Second, interact from other software. Head to r-catmaid <a href="https://natverse.org/rcatmaid/" rel="nofollow noopener noreferrer" target="_blank"><span class="invisible">https://</span><span class="">natverse.org/rcatmaid/</span><span class="invisible"></span></a> (part of the <a href="https://qoto.org/tags/natverse" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>natverse</span></a> suite by Philipp Schlegel <span class="h-card"><a href="https://qoto.org/@uni_matrix" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>uni_matrix</span></a></span>, Alex Bates and others) for an R-based solution from the Jefferis lab at the <a href="https://qoto.org/tags/MRCLMB" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>MRCLMB</span></a>. Includes tools such as <a href="https://qoto.org/tags/NBLAST" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>NBLAST</span></a> for anatomical comparisons of neurons (see paper by Marta Costa et al. 2016 <a href="https://www.sciencedirect.com/science/article/pii/S0896627316302653" rel="nofollow noopener noreferrer" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">sciencedirect.com/science/arti</span><span class="invisible">cle/pii/S0896627316302653</span></a> ).</p><p>If R is not your favourite, then how about <a href="https://qoto.org/tags/python" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>python</span></a>: the <a href="https://qoto.org/tags/navis" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>navis</span></a> package, again by the prolific <span class="h-card"><a href="https://qoto.org/@uni_matrix" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>uni_matrix</span></a></span>, makes it trivial, and works also within <a href="https://qoto.org/tags/Blender" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Blender</span></a> too for fancy 3D renderings and animations. An earlier, simpler version was <a href="https://qoto.org/tags/catpy" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>catpy</span></a> by <span class="h-card"><a href="https://qoto.org/@csdashm" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>csdashm</span></a></span> <a href="https://github.com/ceesem/catpy" rel="nofollow noopener noreferrer" target="_blank"><span class="invisible">https://</span><span class="">github.com/ceesem/catpy</span><span class="invisible"></span></a> , who also has examples on access from <a href="https://qoto.org/tags/matlab" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>matlab</span></a>.</p><p>Third, directly from a <a href="https://qoto.org/tags/psql" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>psql</span></a> prompt. As in, why not? <a href="https://qoto.org/tags/SQL" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>SQL</span></a> is quite a straightforward language. Of course, you'll need privileged access to the server, so this one is only for insiders. Similarly privileged is from an <a href="https://qoto.org/tags/ipython" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>ipython</span></a> prompt initialized via <a href="https://qoto.org/tags/django" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>django</span></a> from the command line, with the entire server-side API at your disposal for queries.</p><p>Fourth, and one of my favourites: from the <a href="https://qoto.org/tags/javascript" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>javascript</span></a> console in the browser itself. There are a handful of examples here <a href="https://github.com/catmaid/CATMAID/wiki/Scripting" rel="nofollow noopener noreferrer" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/catmaid/CATMAID/wik</span><span class="invisible">i/Scripting</span></a> but the possibilities are huge. Key utilities are the "fetchSkeletons" macro-like javascript function <a href="https://github.com/catmaid/CATMAID/wiki/Scripting#count-the-number-of-presynaptic-sites-and-the-number-of-presynaptic-connectors-on-an-axon" rel="nofollow noopener noreferrer" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/catmaid/CATMAID/wik</span><span class="invisible">i/Scripting#count-the-number-of-presynaptic-sites-and-the-number-of-presynaptic-connectors-on-an-axon</span></a> and the NeuronNameService.getInstance().getName(<skeleton_id>) function. </p><p>Notice every <a href="https://qoto.org/tags/CATMAID" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CATMAID</span></a> server has its /apis/, e.g., at <a href="https://l1em.catmaid.virtualflybrain.org/apis/" rel="nofollow noopener noreferrer" target="_blank"><span class="invisible">https://</span><span class="ellipsis">l1em.catmaid.virtualflybrain.o</span><span class="invisible">rg/apis/</span></a> will list all GET or REST server access points. Reach to them as you please. See the documentation: <a href="https://catmaid.readthedocs.io/en/stable/api.html" rel="nofollow noopener noreferrer" target="_blank"><span class="invisible">https://</span><span class="ellipsis">catmaid.readthedocs.io/en/stab</span><span class="invisible">le/api.html</span></a></p><p>In short: the data is there for you to reach out to, interactively or programmatically, and any fine mixture of the two as you see fit.</p>
Albert Cardona<p>(That was <a href="https://qoto.org/tags/VirtualFlyBrain" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>VirtualFlyBrain</span></a>: <a href="http://virtualflybrain.org/" rel="nofollow noopener noreferrer" target="_blank"><span class="invisible">http://</span><span class="">virtualflybrain.org/</span><span class="invisible"></span></a> )</p>
ExploreLive feeds
Mastodon is the best way to keep up with what's happening.
Follow anyone across the fediverse and see it all in chronological order. No algorithms, ads, or clickbait in sight.
Create accountLoginDrag & drop to upload