[ome-users] Naming patterns with Bio-Formats Exporter

[Balaji Ramalingam (Staff)]

Hi Niko,

Thank you for submitting your issue.
Yes this is a known limitation on the Bio-Formats side and we have a
ticket open on this regard,
https://trac.openmicroscopy.org/ome/ticket/12678
And get looked into, at the earliest.

For the time being you could use the following ImageJ/FIJI macro as a
workaround,
This works on the ³current active Image of ImageJ/FIJI².

macro "SplitZSlices [F2]"
{
    run("Bio-Formats Macro Extensions");
    splitZonActiveImage()
}

function splitZonActiveImage()
{
pathToSaveImage = "/Users/bramalingam/Desktop/FIJI_Test/Z²

    dir = getDirectory("image");
     name= getTitle;
     path = dir+name;
     print(path)
    Ext.setId(path)
    Ext.getSizeZ(sizeZ);
    Ext.getSizeT(sizeT);
    for(i=1;i<=sizeZ;i++){

        optionsString = "slices=" + sizeZ + " frames=1-" + sizeT;
        print(optionsString);
        run("Make Substack...", optionsString);
        if (i<10)
            padding = "000";
        else if (i<100)
            padding = "00";
        else
            padding = "";

        print(padding);
        newName = "save=³ + pathToSaveImage + padding + i + ".ome.tif";
        options = newName + " export comp0ression=Uncompressed";
        print(newName);
        run("Bio-Formats Exporter", options);
        close();

    }
    Ext.close();
}


Hope that helps.

Best,
Balaji

__________________
Mr Balaji Ramalingam
Software Developer

OME Team
School of Life Sciences
University of Dundee






On 24/08/2016, 11:21, "ome-users on behalf of Niko Ehrenfeuchter"
<ome-users-bounces at lists.openmicroscopy.org.uk on behalf of
nikolaus.ehrenfeuchter at unibas.ch> wrote:

>Dear all,
>
>is there a way to ask the BF Exporter in Fiji to prefix numbers
>(z-slices in our case) with leading zeros? One of the subsequent tools
>in our workflow is seriously confused about the order of the z-slices
>otherwise.
>
>Thanks a lot,
>Niko
>--
>Niko Ehrenfeuchter | Image Analysis Specialist | Biozentrum, University
>of Basel | Klingelbergstr. 50/70 | CH-4056 Basel
>Phone: +41 (61) 26 72673 | nikolaus.ehrenfeuchter at unibas.ch |
>www.biozentrum.unibas.ch | www.microscopynetwork.unibas.ch
>_______________________________________________
>ome-users mailing list
>ome-users at lists.openmicroscopy.org.uk
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