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" target="_blank">#<span>Platynereis</span></a> larval <a href="https://biologists.social/tags/connectome" class="mention hashtag" rel="nofollow noopener" 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" 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" 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" 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" 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" target="_blank">#<span>CATMAID</span></a> database:</p><p><a href="https://catmaid.jekelylab.ex.ac.uk" rel="nofollow noopener" 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" 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" target="_blank">@<span>biology</span></a></span> <a href="https://biologists.social/tags/volumeEM" class="mention hashtag" rel="nofollow noopener" 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" target="_blank">@<span>biorxivpreprint</span></a></span></p>
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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" 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" 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" target="_blank">#<span>tootprint</span></a> on the preprint from back in the Autumn: <a href="https://mathstodon.xyz/@albertcardona/109422190525090990" rel="nofollow noopener" 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" target="_blank">#<span>CATMAID</span></a> thanks to hosting by the <a href="https://mathstodon.xyz/tags/VirtualFlyBrain" class="mention hashtag" rel="nofollow noopener" 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" 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" target="_blank">#<span>neuroscience</span></a> <a href="https://mathstodon.xyz/tags/connectomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>connectomics</span></a> <a href="https://mathstodon.xyz/tags/Drosophila" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Drosophila</span></a> <a href="https://mathstodon.xyz/tags/DrosophilaLarva" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>DrosophilaLarva</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" target="_blank">#<span>CATMAID</span></a> was devised as "google maps but for volumes". Documentation at <a href="https://catmaid.org" rel="nofollow noopener" 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" 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" target="_blank">#<span>CATMAID</span></a> enables hundreds of <a href="https://mathstodon.xyz/tags/neuroscience" class="mention hashtag" rel="nofollow noopener" 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" target="_blank">#<span>connectome</span></a>.</p><p>See the <a href="https://mathstodon.xyz/tags/Drosophila" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Drosophila</span></a> larval CNS at the <a href="https://mathstodon.xyz/tags/VirtualFlyBrain" class="mention hashtag" rel="nofollow noopener" 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" 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/TrakEM2" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>TrakEM2</span></a> runs as a plugin of <a href="https://mathstodon.xyz/tags/FijiSc" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>FijiSc</span></a> <a href="https://fiji.sc/" rel="nofollow noopener" translate="no" target="_blank"><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="nofollow noopener" target="_blank">#<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="nofollow noopener" target="_blank">#<span>neuroscience</span></a> community.</p><p><a href="https://mathstodon.xyz/tags/TrakEM2" class="mention hashtag" rel="nofollow noopener" target="_blank">#<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="nofollow noopener" target="_blank">#<span>TrakEM2</span></a> was ~16 TB. For larger volumes see <a href="https://mathstodon.xyz/tags/CATMAID" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>CATMAID</span></a>.</p><p>For 3D visualization <a href="https://mathstodon.xyz/tags/TrakEM2" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>TrakEM2</span></a> uses the 3D Viewer <a href="https://imagej.net/plugins/3d-viewer/" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="">imagej.net/plugins/3d-viewer/</span><span class="invisible"></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" 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" 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" 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" 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" 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" 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" 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" 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" 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" target="_blank">#<span>MRCLMB</span></a>. Includes tools such as <a href="https://qoto.org/tags/NBLAST" class="mention hashtag" rel="nofollow noopener" 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" 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" target="_blank">#<span>python</span></a>: the <a href="https://qoto.org/tags/navis" class="mention hashtag" rel="nofollow noopener" 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" 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" 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" target="_blank">#<span>catpy</span></a> by <span class="h-card"><a href="https://qoto.org/@csdashm" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>csdashm</span></a></span> <a href="https://github.com/ceesem/catpy" rel="nofollow noopener" 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" 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" target="_blank">#<span>psql</span></a> prompt. As in, why not? <a href="https://qoto.org/tags/SQL" class="mention hashtag" rel="nofollow noopener" 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" target="_blank">#<span>ipython</span></a> prompt initialized via <a href="https://qoto.org/tags/django" class="mention hashtag" rel="nofollow noopener" 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" 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" 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" 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" target="_blank">#<span>CATMAID</span></a> server has its /apis/, e.g., at <a href="https://l1em.catmaid.virtualflybrain.org/apis/" rel="nofollow noopener" 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" 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>The web-based open source software <a href="https://qoto.org/tags/CATMAID" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>CATMAID</span></a> was devised as "google maps but for volumes". Documentation at <a href="https://catmaid.org" rel="nofollow noopener" 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" 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://qoto.org/tags/CATMAID" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>CATMAID</span></a> enables hundreds of <a href="https://qoto.org/tags/neuroscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>neuroscience</span></a> researchers world wide to collaboratively map neuronal circuits in large datasets, e.g., 100 TB or larger, limited only by bandwidth and server-side storage. The goal: to map and analyse a whole brain <a href="https://qoto.org/tags/connectome" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>connectome</span></a>.</p><p>Running client-side on <a href="https://qoto.org/tags/javascript" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>javascript</span></a> and server-side on <a href="https://qoto.org/tags/django" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>django</span></a> <a href="https://qoto.org/tags/python" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>python</span></a> <a href="https://qoto.org/tags/postgresql" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>postgresql</span></a>, it's a pleasure to use–if I may say so–and easy to hack on to extend its functionality with further widgets.</p><p>The first minimally viable product was produced in 2007 by Stephan Saalfeld (what we now refer to, dearly, as "Ice Age CATMAID), who demonstrated to us all that the web, and javascript, where the way to go for distributed, collaborative annotation of large datasets accessed piece-wise. See the original paper: <a href="https://academic.oup.com/bioinformatics/article-abstract/25/15/1984/210794" rel="nofollow noopener" target="_blank"><span class="invisible">https://</span><span class="ellipsis">academic.oup.com/bioinformatic</span><span class="invisible">s/article-abstract/25/15/1984/210794</span></a></p><p>See also public instances at the <a href="https://qoto.org/tags/VirtulaFlyBrain" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>VirtulaFlyBrain</span></a> <a href="http://virtualflybrain.org/" rel="nofollow noopener" target="_blank"><span class="invisible">http://</span><span class="">virtualflybrain.org/</span><span class="invisible"></span></a> particularly under "tools - CATMAID - hosted EM data such as this <a href="https://qoto.org/tags/Drosophila" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Drosophila</span></a> first instar larval volume of its complete nervous system <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" 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>To fill in my profile tags, a thread:</p><p><a href="https://qoto.org/tags/TrakEM2" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>TrakEM2</span></a> is open source software mostly for <a href="https://qoto.org/tags/connectomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>connectomics</span></a> (but found uses well beyond), and provides the means for both manual and automatic montaging and aligning overlapping 2D image tiles (with <a href="https://qoto.org/tags/SIFT" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>SIFT</span></a> features and rigid or elastic transformation models), and then reconstructing with mostly manual means–by painting with a digital brush–the volumes of structures of interest, as well as trace the branched arbors of e.g., neurons and annotate their synapses, therefore mapping a <a href="https://qoto.org/tags/connectome" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>connectome</span></a> from <a href="https://qoto.org/tags/vEM" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>vEM</span></a> (volume electron microscopy).</p><p><a href="https://qoto.org/tags/TrakEM2" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>TrakEM2</span></a> paper at <a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0038011" rel="nofollow noopener" 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" target="_blank"><span class="invisible">https://</span><span class="">github.com/trakem2/</span><span class="invisible"></span></a></p><p>For 3D visualization, <a href="https://qoto.org/tags/TrakEM2" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>TrakEM2</span></a> uses the 3D Viewer <a href="https://imagej.net/plugins/3d-viewer/" rel="nofollow noopener" target="_blank"><span class="invisible">https://</span><span class="">imagej.net/plugins/3d-viewer/</span><span class="invisible"></span></a></p><p>As software, <a href="https://qoto.org/tags/TrakEM2" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>TrakEM2</span></a> runs as a plugin of <a href="https://qoto.org/tags/FijiSc" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>FijiSc</span></a> <a href="https://fiji.sc/" rel="nofollow noopener" target="_blank"><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://qoto.org/tags/FijiSc" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>FijiSc</span></a> software in the first place, to manage its many dependencies and therefore facilitate distribution to the broader <a href="https://qoto.org/tags/neuroscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>neuroscience</span></a> community.</p><p><a href="https://qoto.org/tags/TrakEM2" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>TrakEM2</span></a> was founded in 2005, when terabyte-sized datasets were rare and considered large. The largest dataset that I've successfully managed with <a href="https://qoto.org/tags/TrakEM2" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>TrakEM2</span></a> was about 16 TB. For larger datasets, see <a href="https://qoto.org/tags/CATMAID" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>CATMAID</span></a> below.</p>
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