Difference between revisions of "MVR-DefineDataset"

(final image)
(Define Dataset 2/3)
 
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In case you selected the option, a list of found files will be presented
 
In case you selected the option, a list of found files will be presented
 
[[File:MVR_define4.png]]
 
[[File:MVR_define4.png]]
 
+
== Define Dataset 3/3 ==
 
Finally the plugin shows you the calibration it read from the files or asks for it.
 
Finally the plugin shows you the calibration it read from the files or asks for it.
 
[[File:MVR_define5.png]]
 
[[File:MVR_define5.png]]
 +
 +
== Log File Output ==
 +
<pre>
 +
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'.
 +
</pre>

Latest revision as of 06:23, 21 August 2014

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'.