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#catmaid — Public Fediverse posts

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

  1. Albert Cardona @[email protected] ·

    "Just use Postgres until it breaks."
    topicpartition.io/blog/postgre

    We are far from that – we use #postgres to power #CATMAID for #connectomics and so far so good.

    "Donald Knuth warned us in 1974 - premature optimization is the root of all evil. ... The point of this article is to show you that this “small scale” number has grown further than what people remember it to be - it can comfortably mean many megabytes per second. We are in a Postgres Renaissance for a reason: Postgres is frequently good enough. Modern NVMEs and cheap RAM allow it to scale absurdly high."

    #connectomics #catmaid #postgres
  2. Albert Cardona @[email protected] ·

    Sometimes one stops to just look at the data. And the software user interface. They are beautiful.

    We are looking at a cross section of the #Drosophila 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.

    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 @herrsaalfeld – 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.

    See our images and fly neurons here, kindly hosted by the #VirtualFlyBrain :
    l1em.catmaid.virtualflybrain.o

    #neuroscience #CATMAID

    #catmaid #neuroscience #virtualflybrain #drosophila
  3. Albert Cardona @[email protected] ·

    @CurrentBiology

    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 #Drosophila, with #CATMAID, in the STEM volume we imaged and they named "Igor". Congrats on seeing this gargantuan project through!

    The whole larval volume of "Igor", including all tissues, is available here, courtesy of the #OpenOrganelle project led by Aubrey Weigel @avweigel at #HHMIJanelia:
    openorganelle.janelia.org/data

    See it at 5x5x35 nm resolution in #neuroglancer: neuroglancer-demo.appspot.com/ (control-minus and control-plus to zoom; mouse click to pan, scroll wheel to browse in Z).

    Will appear at the #VirtualFlyBrain website soon as well.

    There are many more peripheral nervous system components mapped, yet to be published.

    This paper is open access:
    "Serotonergic modulation of swallowing in a complete fly vagus nerve connectome", Schoofs et al. 2024 cell.com/current-biology/fullt

    #neuroscience #connectomics

    #connectomics #neuroscience #virtualflybrain #neuroglancer #hhmijanelia #openorganelle
  4. dancwart @[email protected] ·

    "May I take your order, dear customer... I highly recommend the pancakes"

    #jojosbizarreadventure #jba #parody #OriginalCharacter #catmaid #art #MastoArt

    #jojosbizarreadventure #jba #parody #originalcharacter #catmaid #art
  5. 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
  6. Albert Cardona @[email protected] ·

    @adredish @neuralreckoning @brembs @ScholarNexus

    Likewise for #TrakEM2, #FijiSc and #catmaid software – except we did write papers for them.

    #catmaid #fijisc #trakem2
  7. Albert Cardona @[email protected] ·

    A connectome of the optic lobe of the extremely tiny fairy wasp, Megaphragma sp.

    "A complete reconstruction of the early visual system of an adult insect", by Chua et al. 2023 (Chklovskii & Polilov) sciencedirect.com/science/arti

    Don't miss the supplemental figures.

    "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
    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."

    Volume assembled with #FijiSc and #TrakEM2, and its neurons and synapses mapped with #CATMAID. Woohoo!

    #neuroscience #connectomics #VolumeEM #vEM #insects #miniaturization

    #miniaturization #insects #vem #volumeem #connectomics #neuroscience
  8. Albert Cardona @[email protected] ·

    Today the peer-reviewed version of our preprint is out:

    "The #connectome of an insect brain"
    science.org/doi/10.1126/scienc

    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.

    See my #tootprint on the preprint from back in the Autumn: mathstodon.xyz/@albertcardona/

    The data is available both as supplements and directly via #CATMAID thanks to hosting by the #VirtualFlyBrain:
    l1em.catmaid.virtualflybrain.o)

    (The "Winding, Pedigo et al. 2023" annotation listing all included neurons will appear very soon in an upcoming update.)

    #neuroscience #connectomics #Drosophila #DrosophilaLarva

    #drosophilalarva #drosophila #connectomics #neuroscience #virtualflybrain #catmaid
  9. Albert Cardona @[email protected] ·

    @remenca @spla @marcbeldata

    Doncs ...

    #BigStitcher nature.com/articles/s41592-019

    #BigDataViewer nature.com/articles/nmeth.3392

    #ImgLib2 academic.oup.com/bioinformatic

    #CATMAID academic.oup.com/bioinformatic

    Elastic volume registration nature.com/articles/nmeth.2072

    #vEM #volumeEM l1em.catmaid.virtualflybrain.o

    #bigstitcher #bigdataviewer #imglib2 #catmaid #vem #volumeem
  10. Albert Cardona @[email protected] ·

    @remenca @spla @marcbeldata

    Doncs ...

    #BigStitcher nature.com/articles/s41592-019

    #BigDataViewer nature.com/articles/nmeth.3392

    #ImgLib2 academic.oup.com/bioinformatic

    #CATMAID academic.oup.com/bioinformatic

    Elastic volume registration nature.com/articles/nmeth.2072

    #vEM #volumeEM l1em.catmaid.virtualflybrain.o

    #bigstitcher #bigdataviewer #imglib2 #catmaid #vem #volumeem
  11. Albert Cardona @[email protected] ·

    @remenca @spla @marcbeldata

    Doncs ...

    #BigStitcher nature.com/articles/s41592-019

    #BigDataViewer nature.com/articles/nmeth.3392

    #ImgLib2 academic.oup.com/bioinformatic

    #CATMAID academic.oup.com/bioinformatic

    Elastic volume registration nature.com/articles/nmeth.2072

    #vEM #volumeEM l1em.catmaid.virtualflybrain.o

    #volumeem #vem #catmaid #imglib2 #bigdataviewer #bigstitcher
  12. Albert Cardona @[email protected] ·

    @remenca @spla @marcbeldata

    Doncs ...

    #BigStitcher nature.com/articles/s41592-019

    #BigDataViewer nature.com/articles/nmeth.3392

    #ImgLib2 academic.oup.com/bioinformatic

    #CATMAID academic.oup.com/bioinformatic

    Elastic volume registration nature.com/articles/nmeth.2072

    #vEM #volumeEM l1em.catmaid.virtualflybrain.o

    #bigstitcher #bigdataviewer #imglib2 #catmaid #vem #volumeem
  13. Albert Cardona @[email protected] ·

    @dantracey @kristinmbranson @annikabarber @debivort @giorgiogilestro

    Find the original basin-1 neurons at the #VirtualFlyBrain at "Tools - CATMAID - Hosted EM Data - Larval - Larva (ABD1.5)" which opens a #CATMAID server abd1.5.catmaid.virtualflybrain)

    Find them via Neuron Search (icon with a "?").

    The "Construction time" is wrong (see "Summary info" of the Selection Table) because these neurons were imported from #TrakEM2. Old enough to predate the #CATMAID software!
    #neuroscience

    #trakem2 #catmaid #virtualflybrain #neuroscience
  14. Albert Cardona @[email protected] ·

    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.

    This work started at #HHMIJanelia and continued at the #MRCLMB in Cambridge, UK.

    All neuron reconstructions were done painstakingly by hand with #CATMAID by over >80 people! Thanks so much!

    #neuroscience #connectomics
    /END

    #connectomics #neuroscience #catmaid #mrclmb #hhmijanelia
  15. Albert Cardona @[email protected] ·

    The web-based open source software #CATMAID was devised as "google maps but for volumes". Documentation at catmaid.org and source code at github.com/catmaid/CATMAID/

    Modern #CATMAID enables hundreds of #neuroscience 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 #connectome.

    See the #Drosophila larval CNS at the #VirtualFlyBrain server: l1em.catmaid.virtualflybrain.o)

    #virtualflybrain #drosophila #connectome #neuroscience #catmaid
  16. 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
  17. Albert Cardona @[email protected] ·

    Have you visited the #FlyWire website yet? Both for helping proofread and analyze the whole #Drosophila brain #connectome, or simply to admire the beautiful renderings of neuronal arbors: join.flywire.ai

    (See also the #VirtualFlyBrain for #ontology-driven navigation of the fly brain, and access to images of genetic driver lines, and more: v2.virtualflybrain.org/org.gep )

    Wish I had time or resources to create such a beautiful landing page for the larval central nervous system. The #connectome of the whole larval brain is coming soon. For now, see the #vEM images and some ~3,000 published neurons in this #CATMAID server: l1em.catmaid.virtualflybrain.o)

    #connectomics

    #connectome #virtualflybrain #flywire #drosophila #ontology #vem
  18. Albert Cardona @[email protected] ·

    Have you visited the #FlyWire website yet? Both for helping proofread and analyze the whole #Drosophila brain #connectome, or simply to admire the beautiful renderings of neuronal arbors: join.flywire.ai

    (See also the #VirtualFlyBrain for #ontology-driven navigation of the fly brain, and access to images of genetic driver lines, and more: v2.virtualflybrain.org/org.gep )

    Wish I had time or resources to create such a beautiful landing page for the larval central nervous system. The #connectome of the whole larval brain is coming soon. For now, see the #vEM images and some ~3,000 published neurons in this #CATMAID server: l1em.catmaid.virtualflybrain.o)

    #connectomics

    #connectome #virtualflybrain #flywire #drosophila #ontology #vem
  19. Albert Cardona @[email protected] ·

    Have you visited the #FlyWire website yet? Both for helping proofread and analyze the whole #Drosophila brain #connectome, or simply to admire the beautiful renderings of neuronal arbors: join.flywire.ai

    (See also the #VirtualFlyBrain for #ontology-driven navigation of the fly brain, and access to images of genetic driver lines, and more: v2.virtualflybrain.org/org.gep )

    Wish I had time or resources to create such a beautiful landing page for the larval central nervous system. The #connectome of the whole larval brain is coming soon. For now, see the #vEM images and some ~3,000 published neurons in this #CATMAID server: l1em.catmaid.virtualflybrain.o)

    #connectomics

    #connectomics #catmaid #vem #ontology #drosophila #flywire
  20. 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
  21. Albert Cardona @[email protected] ·

    To fill in my profile tags, a thread:

    #TrakEM2 is open source software mostly for #connectomics (but found uses well beyond), and provides the means for both manual and automatic montaging and aligning overlapping 2D image tiles (with #SIFT 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 #connectome from #vEM (volume electron microscopy).

    #TrakEM2 paper at journals.plos.org/plosone/arti

    Git repository at github.com/trakem2/

    For 3D visualization, #TrakEM2 uses the 3D Viewer imagej.net/plugins/3d-viewer/

    As software, #TrakEM2 runs as a plugin of #FijiSc fiji.sc/ and in fact motivated the creation of the #FijiSc software in the first place, to manage its many dependencies and therefore facilitate distribution to the broader #neuroscience community.

    #TrakEM2 was founded in 2005, when terabyte-sized datasets were rare and considered large. The largest dataset that I've successfully managed with #TrakEM2 was about 16 TB. For larger datasets, see #CATMAID below.

    #connectomics #sift #connectome #trakem2 #vem #fijisc
  22. Albert Cardona @[email protected] ·

    Above, my #introduction of interests. Here, who I am, what I do: a neuroscientist at the #MRCLMB and University of Cambridge, UK, studying the neural circuit basis of behavior, originally in #Drosophila but now also in #cephalopods (#pygmysquid #Idiosepius), the lancelet #Amphioxus and other animals. Our main approach: whole brain #connectomics with #vEM (volume electron microscopy) as the basis for computational modeling to guide neuronal activity perturbation and monitoring experiments with #optogenetics and #electrophysiology (#ephys for short).
    Once upon a time I founded the #ImageJ -based #TrakEM2 software for image registration and neuronal arbor reconstruction and annotation, which spurred founding the #FijiSc (fiji.sc) image processing software, and later the #CATMAID web-based software for #connectomics.
    Always open to inquires from prospective students and postdocs, and collaborations.

    #introduction #vem #optogenetics #electrophysiology #ephys #imagej