Run ICY from commandline with script or protocol parameters on Ubunutu

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  • sebi06 March 24, 2020 at 9:24 am

    Hi,

    as demonstrated on the NEUBIAS just a few weeks ago our ZEN blue and ZEN core software allows to integrate Docker Container to create custom workflows. This works fine for many ImageJ / Fiji plugins, but I would like to do the same

    • by creating a ICY protocol or script
    • packaging ICY + script / protocol into a container –> maybe there is already a ICY container
    • convert it to an APEER module
    • run it locally inside ZEN and enjoy

    Any help would be really appreciated.

    Sebi (from ZEISS)

    • This topic was modified 4 years, 9 months ago by
      sebi06      .
    Marion Louveaux March 26, 2020 at 12:34 pm

    Dear Sebi06,

    A few quick elements of answer here:
    It is possible to run an Icy protocol or a JavaScript via the command line:
    – protocols: https://icy.bioimageanalysis.org/plugin/protocols/
    – JavaScript: https://icy.bioimageanalysis.org/plugin/command-line-script-runner/
    It is possible to include a Docker container in an Icy plugin https://icy.bioimageanalysis.org/plugin/docker-for-icy/
    And there seems to be a Docker container for Icy: https://icy.bioimageanalysis.org/plugin/icyhlplugininstaller/

    The Icy development team is eager to help you converting Icy plugins or protocols to APEER modules and document this procedure for Icy/Zeiss users. I would suggest that we discuss this further by chat. Could you contact me by email to set a chat appointment?

    Best regards,
    Marion
    sebi06 March 31, 2020 at 12:47 pm

    Hi Marion,

    since I do not have your mail I give you mine to get in contact data from  my work email.

    sebastian.rhode@zeiss.com

    Cheers,

    Sebi

    ——————————————————————————

    Dr. Sebastian Rhode

    Product Manager/Product Owner – Machine Learning

    Staff Expert

    Technology Center Software

    ZEISS Research Microscopy Solutions
    Carl Zeiss Microscopy GmbH

    Kistlerhofstr. 75

    81379 München, GermanyPhone: +49 89 90 9000 313

    Mobil:   +49 151 46178900
    sebastian.rhode@zeiss.com
    http://www.zeiss.com/microscopy

     

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