Load a 3D binary mask into the MaskEditor plugin

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  • MicheleGriffa July 8, 2019 at 10:40 am

    Dear Icy developers and users,

    as a new Icy user I may post here a silly and trivial question. My apologies in advance if that is the case.

    I have a 3D binary mask saved as a single TIFF file stack of 8-bit unsigned integer 2D images. I produced such stack with a certain segmentation procedure (in this case Icy’s Active Contours plugin).

    Is it possible to load such a stack into Icy’s MaskEditor plugin such that I can visualize the binary mask on top of the original 16-bit unsigned integer stack it was produced from by segmentation?

    I tried to load the TIFF stack file into MaskEditor but an error was returned (already sent via the error reporting of Icy).

    Does the MaskEditor plugin work only with 2D binary mask files or also with stacks thereof?

    If 3D binary masks can be used as well, how could they be loaded?

    Thanks in advance for any feedback.

    Best regards.

    Michele

    Stephane Dallongeville July 8, 2019 at 4:55 pm

    Dear Michele,

    The usual way of getting segmentation results in Icy is to use the ROI (Region Of Interest) export (Active Contours does has it) so it will display those ROI masks directly on the original image as you wanted (and you can get them displayed in 3D too).

    Hope that is what you’re looking for.

    Best,

    – Stephane

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