Stitching / mosaic / grid creation from a series / stack

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    Jacob Martin September 17, 2019 at 5:28 pm

    I am brand new to Icy and I apologize if this is answered somewhere but I couldn’t find anything.

    I have a large number of Leica confocal .lif series files which I am having trouble loading the way I want. The images are all captured as a large grid with a certain amount of overlap between each successive image, and rather than displaying the series as a z-stack or time series I want to “stitch” the images together into a larger 2D image (Leica calls this creating a “mosaic” in their software).

    Could someone please help me convert the series to display correctly? I believe the images were captured such that they snake back and forth:

    Line 1 left to right

    Line 2 right to left

    Line 3 left to right

    and so on.

    Thank you for the help!

    Stephane Dallongeville September 17, 2019 at 6:11 pm

    Hi Jacob,

    Normally Icy should automatically stitch the image when you select “group files” in the loading dialog :

    Still that will be a very basic stitching without considering overlap area, and it works only if all the images contained in the multi-series file have all the exact same size. For instance in my case above the multi-series file contains a preview image with a different size so stitching doesn’t operate.

    If you want an advanced stitching tool you may try this :

    https://imagej.net/Image_Stitching

    As i don’t think Icy contains that kind of tool.

    Best,

    – Stephane

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