possible to run Potts Segmentation on stacks / multiple images?

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  • Stefan Fischer October 27, 2019 at 8:06 pm

    Hi all,

    I was testing the Plugin “Potts Segmentation” today and found it quite valuable for one of my projects. Everything works fine so far on single images, but I need to run it on multiple images or on a image stack.  If I run it on a tiff stack, it only takes the first slice of the stack. The plugin is not included in the blocks in the Protocols editor, thus I can not loop it through a folder. Any ideas on how to get it run on multiple images?

    Thanks for your help,

    Stefan

     

     

    Stephane Dallongeville October 29, 2019 at 9:44 am

    Hi Stefan,

    This plugin has been developed by EPFL group, you may try to reach the original author from the plugin page to see if he can help:

    Potts Segmentation

    Best,

    – Stephane

    Stefan Fischer October 29, 2019 at 10:28 am

    Hi Stephane,

    thanks for your answer, I did exactly that in parallel. I just wanted to make sure that I am not missing a possibility in ICY and will post any information / solution that I receive from the EPFL group back into this post here to make it visible for everybody.

    Best,

    Stefan

    Stephane Dallongeville October 29, 2019 at 12:38 pm

    Thanks, that would be really useful indeed !

    Best,

    – Stephane

    Stefan Fischer November 12, 2019 at 8:33 pm

    Hi all,

    I now received the answer from the author of the plugin that a change within the plugin to support image stacks (or multiple images) would require a change in the core of the procedure, which would be a quite demanding task. The author therefore proposed to use the plugin as is instead and loop it through a folder of images using the protocols editor. The question would then only be how can it be made available in the blocks (where it is not yet to be found)? I was told that this is not controlled by the plugin developers, but centrally by Icy.

    Any ideas?

    Best,

    Stefan

    Stefan Fischer November 25, 2019 at 8:54 pm

    Hi all,

    quick update: I just received the notification that “Potts Segmentation” was added to the blocks in the protocols editor in the recent update, thanks to joined work of Vasileios Angelopoulos  (plugin author) and the Icy Team. Thus it is now accessible to run it on multiple images in batch.

    Thanks a lot for your help and support!!

    Best,

    Stefan

     

    Stephane Dallongeville November 26, 2019 at 6:37 pm

    Hi Stefan,

    Even if the reply come too late, it may still be useful for developers: the plugin needs to implement a specific interface called Block to be compatible with Protocols so it’s up to the developer to do it. Hopefully when you’re using EzPlug, the Protocols implementation should be really fast and straightforward 🙂

    Cheers,

    – Stephane

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