MVR-DefineDataset

Select Type of Dataset

MVR define1.png

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

MVR define2.png

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

MVR define3.png

In case you selected the option, a list of found files will be presented MVR define4.png

Define Dataset 3/3

Finally the plugin shows you the calibration it read from the files or asks for it. MVR define5.png

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'.