This is an archive of the old MediaWiki-based ImageJ wiki. The current website can be found at imagej.net.
MVR-DefineDataset
Contents
Select Type of Dataset
Error creating thumbnail: Unable to save thumbnail to destination
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
Error creating thumbnail: Unable to save thumbnail to destination
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
- 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
- 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
Error creating thumbnail: Unable to save thumbnail to destination
In case you selected the option, a list of found files will be presented
Error creating thumbnail: Unable to save thumbnail to destination
Define Dataset 3/3
Finally the plugin shows you the calibration it read from the files or asks for it.
Error creating thumbnail: Unable to save thumbnail to destination
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'.
