Stitching / mosaic / grid creation from a series / stack

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  • Jacob Martin

    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

    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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