Replies Created

  • Marion Louveaux

    Dear Nigel Keeley

    We migrated on the image.sc forum and this forum is now closed. You can get more info here.

    Could you please re-post your question on the image.sc forum and in the optionnal tags, write “icy”? This way the Icy team, but also the whole bioimage analysis community can help you and benefit from the answer.

    When re-posting, could also upload an example of image you would like to process?

    As you say that you are new to image analysis and Icy in particular, I take the opportunity to mention the webinar I made for NEUBIAS Academy @home on Icy:

    Video
    Slides
    Q&A

    Many thanks in advance and see you soon on the image.sc forum!

    Best regards,

    Marion, for the Icy team

    Marion Louveaux

    Dear Maria Parreira,

    We migrated on the image.sc forum and this forum is now closed. You can get more info here.

    Could you please re-post your question on the image forum and in the optionnal tags, write “icy”? This way the Icy team, but also the whole bioimage analysis community can help you and benefit from the answer.

    As you say that you are new to image analysis and Icy in particular, I take the opportunity to mention the webinar I made for NEUBIAS Academy @home on Icy:

    Video
    Slides
    Q&A

    And to mention the tutorial on Active Contour that my colleagues recently published.

    Many thanks in advance and see you soon on the image.sc forum!

    Best regards,

    Marion, for the Icy team

    Marion Louveaux

    Dear Dariana Torres Rivera,

    We migrated on the image.sc forum and this forum is now closed. You can get more info here: http://icy.bioimageanalysis.org/support/topic/icy-forum-is-closed/

    Could you re-post the description of the issue you encountered on https://forum.image.sc/ with the tag “icy”  ? On top of the information you already provided, it would be helpful for us to know the Icy version you use (bottom right corner of the graphical user interface), to have the content of the “Output” tab just after starting Icy (right side panel) and to see a screenshot of the exact error message you see when the system crashes.

    Many thanks in advance and see you soon on the image.sc forum.

    Best regards,

    Marion, for the Icy team

    Marion Louveaux

    Dear Jose M Adrover,

    Thank you for contributing to this thread on 3D VTK.

    We migrated on the image.sc forum and this forum is now closed. You can get more info here: http://icy.bioimageanalysis.org/support/topic/icy-forum-is-closed/

    Could you open a new thread on https://forum.image.sc/ with the tag “icy” about this topic and re-post the description of the issue you encountered (with the Icy version)?

    Many thanks in advance.

    Best regards

    Marion, for the Icy team

    Marion Louveaux

    Dear Frederic,

    As announced here, we migrated on the image.sc forum. This forum is now closed. Please post your questions on the image.sc forum using the tag “icy”.

    Thank you for being an active Icy user!

    Best regards,

    Marion

    Marion Louveaux

    To follow all “icy” related topics on the Image.sc forum, go to your profile, then in the Preferences -> Notifications -> Tags and write “icy” in the watched tags:

    Marion Louveaux

    When posting a message on the Image.sc forum, don’t forget to add the tag “Icy”.

    Use the following categories for the following topics:

    “Image Analysis” ->general questions on how to analyse an image

    “Usage & Issues” -> issues with a plugin, bug report

    “Development” -> feature request

    Marion Louveaux

    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: http://icy.bioimageanalysis.org/plugin/protocols/
    – JavaScript: http://icy.bioimageanalysis.org/plugin/command-line-script-runner/
    It is possible to include a Docker container in an Icy plugin http://icy.bioimageanalysis.org/plugin/docker-for-icy/
    And there seems to be a Docker container for Icy: http://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

    Marion Louveaux

    Dear Xavier,

    I have no experience with Amira or Blender, but a colleague told me that it is possible to export Amira files to .obj or .stl instead of .am and that Blender can import .stl or .obj.
    See here for Amira documentation: http://avsl.cct.lsu.edu/vizclass_illustration.html#save-individual-surface-and-export-to-desirable-format
    I hope it solves your issue.

    Best regards,
    Marion

    Marion Louveaux

    Dear Michel Kress,
    The Auto-adjust size option is probably unticked. Go to Layer panel -> Scale bar layer to modify this option. I attached a screenshot of this panel for Icy version 2.0.3.0.
    Best regards,
    Marion

    Layer Panel