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MVR-DefineDataset

    Select Type of Dataset

    There are three types of datasets:

    • Image Stacks (LOCI Bioformats)
      • to open non TIFF images
    • Image Stacks (ImageJ Opener)
      • use this to open TIFF and zipped TIFFS
    • Zeiss Lightsheet Z.1 Dataset
      • experimental way of opening Zeiss data

    Define Dataset 1/3

    This dialog specifies of what your dataset consists of:

    • timepoints
    • channels
    • illumination directions
    • angles

    Define Dataset 2/3

    This dialog asks you several facts:

    • image directory
    • image file pattern
      • there are 3 different variables. They are used to identify the images. All of them can have leading zeros, e.g. {aaa} for a angle of 045 degrees or {tttt} for 0014 as a time point
        • {t} - time points
        • {c} - channel
        • {a} - angles
    • time points, channels and angles can be given as a comma seperated list or in a more elegant way, {start}-{end}:{interval}
    • calibration can be either read from file or entered by hand
    • data container, smaller image stacks can use ArrayImg, bigger one should use CellImg

    In case you selected the option, a list of found files will be presented

    Define Dataset 3/3

    Finally the plugin shows you the calibration it read from the files or asks for it.

    Log File Output

    Dimensions of viewsetup 0 unknown. Loading them ... 
    Image stack size of first stack: 1388x1040x81
    Dimensions of viewsetup 1 unknown. Loading them ... 
    Image stack size of first stack: 1388x1040x91
    Dimensions of viewsetup 2 unknown. Loading them ... 
    Image stack size of first stack: 1388x1040x102
    Dimensions of viewsetup 3 unknown. Loading them ... 
    Image stack size of first stack: 1388x1040x91
    Dimensions of viewsetup 4 unknown. Loading them ... 
    Image stack size of first stack: 1388x1040x101
    Dimensions of viewsetup 5 unknown. Loading them ... 
    Image stack size of first stack: 1388x1040x91
    Dimensions of viewsetup 6 unknown. Loading them ... 
    Image stack size of first stack: 1388x1040x111
    (Thu Aug 21 13:35:38 CEST 2014): Saved xml '/Users/janosch/no_backup/HisYFP/./dataset_orig.xml'.