TransformJ: Options

General Description

This plugin enables setting global parameters used by the other plugins in the TransformJ package.

Description of Dialog Components

Adopt brightness/contrast from input images. If selected, result images are displayed with the same brightness and contrast settings as the corresponding input images. Otherwise the brightness and contrast will be set such that the maximum result value is mapped to the maximum displayable value, and the minimum result value is mapped to the minimum displayable value.

Close input images after transforming. If selected, ImageJ always closes the input image processed by a TransformJ plugin, after the plugin has finished. This is useful when you need only the result images and not the original input images.

Save result images before closing. If selected, ImageJ always asks whether or not you want to save result images before they are closed. This is useful when you want to exclude the possibility of accidentally closing an image.

Log messaging. If selected, the TransformJ plugins will generate log messages, which appear in the log window of ImageJ. These messages give you more details on what is going on behind the scene.

Notes regarding log messages: most of them originate from the ImageScience library. In this library, the "c-dimension" (channel index) is called the "s-dimension" (spectral parameter). Also, indexing of image elements always starts at 0, as opposed to ImageJ and Image5D, which start at 1 in the z-, t-, and c-dimension. Thus, in the log window, index values for these dimensions entered into the Crop or Embed dialog are reported shifted by 1.

Upon pressing "OK", the options are stored by ImageJ and saved to its preferences file when quitting. Every time a TransformJ plugin is used, these preferences are used. This facilitates adapting the behavior of the package to your wishes.