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#catmaid — Public Fediverse posts

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  1. If your server uses the django framework, beware of SIGPIPE calls:
    github.com/catmaid/CATMAID/com

    In #catmaid we were seeing lots of uwsgi processes going rogue, turns out they were stuck in a loop. Tom Kazimiers successfully figured this out and found a configuration to avoid the issue.

    #python #django

  2. If your server uses the django framework, beware of SIGPIPE calls:
    github.com/catmaid/CATMAID/com

    In #catmaid we were seeing lots of uwsgi processes going rogue, turns out they were stuck in a loop. Tom Kazimiers successfully figured this out and found a configuration to avoid the issue.

    #python #django

  3. If your server uses the django framework, beware of SIGPIPE calls:
    github.com/catmaid/CATMAID/com

    In #catmaid we were seeing lots of uwsgi processes going rogue, turns out they were stuck in a loop. Tom Kazimiers successfully figured this out and found a configuration to avoid the issue.

    #python #django

  4. If your server uses the django framework, beware of SIGPIPE calls:
    github.com/catmaid/CATMAID/com

    In #catmaid we were seeing lots of uwsgi processes going rogue, turns out they were stuck in a loop. Tom Kazimiers successfully figured this out and found a configuration to avoid the issue.

    #python #django

  5. If your server uses the django framework, beware of SIGPIPE calls:
    github.com/catmaid/CATMAID/com

    In #catmaid we were seeing lots of uwsgi processes going rogue, turns out they were stuck in a loop. Tom Kazimiers successfully figured this out and found a configuration to avoid the issue.

    #python #django

  6. "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."

  7. "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."

  8. "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."

  9. "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."

  10. "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."

  11. Happy Pancake Thursday!

    I'm busy preparing for a trip, so I've had very little time for art lately. But that's no excuse to not honour the tradition.

    Drawn in paint using a mouse

    #pancakethursday #pancakes #cat #kemonomimi #catmaid #microsoftpaint #art #MastoArt

  12. Happy Pancake Thursday!

    I'm busy preparing for a trip, so I've had very little time for art lately. But that's no excuse to not honour the tradition.

    Drawn in paint using a mouse

    #pancakethursday #pancakes #cat #kemonomimi #catmaid #microsoftpaint #art #MastoArt

  13. Happy Pancake Thursday!

    I'm busy preparing for a trip, so I've had very little time for art lately. But that's no excuse to not honour the tradition.

    Drawn in paint using a mouse

    #pancakethursday #pancakes #cat #kemonomimi #catmaid #microsoftpaint #art #MastoArt

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. Today maid is very proud to present you my masters castle 😊😊🩷🩷 #uwu #fyu #cosplay #kawaiigirl #maids #catmaid

  20. Today maid is very proud to present you my masters castle 😊😊🩷🩷 #uwu #fyu #cosplay #kawaiigirl #maids #catmaid

  21. @uni_matrix @davi

    ps: also includes nice paragraph on #TrakEM2 by @albertcardona et al. w/ remark on alignments errors auto correction.

    As for #catmaid collaborative annotation & neuronal structures skeletons approach!

  22. @uni_matrix @davi

    ps: also includes nice paragraph on #TrakEM2 by @albertcardona et al. w/ remark on alignments errors auto correction.

    As for #catmaid collaborative annotation & neuronal structures skeletons approach!

  23. @uni_matrix @davi

    ps: also includes nice paragraph on #TrakEM2 by @albertcardona et al. w/ remark on alignments errors auto correction.

    As for #catmaid collaborative annotation & neuronal structures skeletons approach!

  24. @uni_matrix @davi

    ps: also includes nice paragraph on #TrakEM2 by @albertcardona et al. w/ remark on alignments errors auto correction.

    As for #catmaid collaborative annotation & neuronal structures skeletons approach!

  25. @uni_matrix @davi

    ps: also includes nice paragraph on #TrakEM2 by @albertcardona et al. w/ remark on alignments errors auto correction.

    As for #catmaid collaborative annotation & neuronal structures skeletons approach!

  26. @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

  27. @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

  28. @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

  29. @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

  30. @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

  31. @Raf

    El PostGIS funciona de meravella. Fa anys i panys que el fem servir per a la base de dades de #CATMAID, el nostre programari lliure per a mapar neurones en volums de sistemes nerviosos:
    catmaid.readthedocs.io/

  32. @Raf

    El PostGIS funciona de meravella. Fa anys i panys que el fem servir per a la base de dades de #CATMAID, el nostre programari lliure per a mapar neurones en volums de sistemes nerviosos:
    catmaid.readthedocs.io/

  33. @Raf

    El PostGIS funciona de meravella. Fa anys i panys que el fem servir per a la base de dades de #CATMAID, el nostre programari lliure per a mapar neurones en volums de sistemes nerviosos:
    catmaid.readthedocs.io/

  34. @Raf

    El PostGIS funciona de meravella. Fa anys i panys que el fem servir per a la base de dades de #CATMAID, el nostre programari lliure per a mapar neurones en volums de sistemes nerviosos:
    catmaid.readthedocs.io/

  35. @Raf

    El PostGIS funciona de meravella. Fa anys i panys que el fem servir per a la base de dades de #CATMAID, el nostre programari lliure per a mapar neurones en volums de sistemes nerviosos:
    catmaid.readthedocs.io/

  36. 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

  37. 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

  38. 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

  39. 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

  40. 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

  41. Happy Pancake Thursday!

    I've learned that Hellboy likes cats, too, so here's a follow-up of last weeks post.

    #hellboy #PancakeThursday #cats #CatMaid #MaidOutfit #catboy #catgirl #catcafé #cafe #pancakes #myart #art #MastoArt