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'.

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