home.social

#catmaid — Public Fediverse posts

Live and recent posts from across the Fediverse tagged #catmaid, aggregated by home.social.

  1. Gaspar Jekely @[email protected] ·

    We have now published a new and massively extended/reworked preprint of the whole-body #Platynereis larval #connectome with over 50 figures

    biorxiv.org/content/10.1101/20

    All the analyses, plots and figures should be reproducible in #rstats with the code provided:

    zenodo.org/doi/10.5281/zenodo.

    @zenodo_org

    by querying our public #CATMAID database:

    catmaid.jekelylab.ex.ac.uk

    #neuroscience @biology #volumeEM
    @biorxivpreprint

    #platynereis #connectome #rstats #catmaid #neuroscience #volumeem
  2. Albert Cardona @[email protected] ·

    @manlius Yes, a lot, but generated mostly with #CATMAID which is more purpose-built for #connectomics.

    An early reconstruction of a neural circuit done with #TrakEM2 was by Davi Bock et al. 2011 on the mouse visual cortex, "Network anatomy and in vivo physiology of visual cortical neurons" nature.com/articles/nature0980

    Another one with #TrakEM2 was by Dan Bumbarger et al. 2013 "System-wide rewiring underlies behavioral differences in predatory and bacterial-feeding nematodes" where they compared #celegans with another nematode, #pristionchus pacificus that has the exact same amount of neurons but connected differently sciencedirect.com/science/arti

    Later ones with #CATMAID include:

    The polychaete worm #Platynereis by @jekely 's group, "Whole-animal #connectome and cell-type complement of the three-segmented Platynereis dumerilii larva" Verazto et al. 2020 biorxiv.org/content/10.1101/20

    And all of ours in #Drosophila larva. See the #VirtualFlyBrain server which hosts the #vEM of the whole central nervous system and lists all the neurons included in each published paper (currently 23), shared among the papers and all connecting to each other: l1em.catmaid.virtualflybrain.o)

    The 24th will come soon, featuring the complete whole #Drosophila larval brain with ~2,500 neurons. It's under review.

    #catmaid #celegans #pristionchus #platynereis #connectome #drosophila
  3. Albert Cardona @[email protected] ·

    What can you do with a #CATMAID server? Say, let's look at the #Drosophila (vinegar fly, often referred to as fruit fly) larval central nervous system, generously hosted by the #VirtualFlyBrain l1em.catmaid.virtualflybrain.o) or the #Platynereis (a marine annelid) server from the Jekely lab catmaid.jekelylab.ex.ac.uk/

    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.

    Second, interact from other software. Head to r-catmaid natverse.org/rcatmaid/ (part of the #natverse suite by Philipp Schlegel @uni_matrix, Alex Bates and others) for an R-based solution from the Jefferis lab at the #MRCLMB. Includes tools such as #NBLAST for anatomical comparisons of neurons (see paper by Marta Costa et al. 2016 sciencedirect.com/science/arti ).

    If R is not your favourite, then how about #python: the #navis package, again by the prolific @uni_matrix, makes it trivial, and works also within #Blender too for fancy 3D renderings and animations. An earlier, simpler version was #catpy by @csdashm github.com/ceesem/catpy , who also has examples on access from #matlab.

    Third, directly from a #psql prompt. As in, why not? #SQL 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 #ipython prompt initialized via #django from the command line, with the entire server-side API at your disposal for queries.

    Fourth, and one of my favourites: from the #javascript console in the browser itself. There are a handful of examples here github.com/catmaid/CATMAID/wik but the possibilities are huge. Key utilities are the "fetchSkeletons" macro-like javascript function github.com/catmaid/CATMAID/wik and the NeuronNameService.getInstance().getName(<skeleton_id>) function.

    Notice every #CATMAID server has its /apis/, e.g., at l1em.catmaid.virtualflybrain.o will list all GET or REST server access points. Reach to them as you please. See the documentation: catmaid.readthedocs.io/en/stab

    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.

    #drosophila #natverse #mrclmb #django #javascript #virtualflybrain