merge channels

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  • DavidG

    Hi everyone,

     

    I’m looking for a protocol that would merge three channels and save the merged sequence as a TIFF, in batch mode.

    I can not find a merge channel bloc, do you think it would be possible to make one please? It would be super useful!

     

    Many thanks in advance for your help!

     

    David

    Stephane Dallongeville

    Hi David,

    The question is: from where do these 3 channels come from ?
    From different image i guess, so you probably have a specific naming convention for that.
    Merging channels is easy but doing it in batch means that you have to deal with filename parsing to correctly read channel from each image and correctly merge them. It’s always specific, it’s why you don’t see any batch channel merging protocol.

    Best,

    – Stephane

    DavidG

    Thanks Stephane, I understand about name parsing. In the end I did it with FIJI and by merging files ordered in a precise way:

    file01_ch0

    file01_ch1

    file01_ch2, etc

    and merging files in groups of 3. If they are in the right order it works well.

     

    Still, do you think a merge channel bloc would be useful for protocols maybe?

     

    Also, another question:

    In a protocol, I get a 3D ROI for the whole cell, coming from HK-means, but that has gaps in it. Some of these gaps are filled by ‘Fill in Holes in ROI’, but not all of them.

    What is the easiest way of filling all the ROI in?

    I got around it by dilating the ROI along x, y and z, and that filled some of the smaller gaps, but not all.

     

    Is there a way to get the outline of a 3D ROI (i.e. the 3D border) and then filling it in completely maybe?

     

    Many thanks!

     

    David

     

     

     

     

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