Author:	Peter Stierlen (peter.stierlen@t-online.de)
History:	2007/11/28: first version
Source:	ROI_threshold.java
Installation:	Download ROI_threshold.class to the plugins folder and restart ImageJ.
Description:	This plugin allows you to selectively threshold ROIs from stack images and copy the results into the target image.

Threshold of Images with the Plugin ROI_Threshold

This plugin was originally written for the preprocessing of images of optical calibration patterns. The semi-automatic process allows the selection of a polygonal ROI, copy it into the clipboard, threshold the clipboard and copy the black pixels within the ROI from the clipboard into the target image. The target image is automatically generated in the same size as the source image.

Open source image

Start Plugin ROI_Threshold

Source and target image are placed automatically

The Polygon-Selection Tool will be pre-selected. The target image (resp. target stack if the source is a stack) is generated in the original source size. Choose within the source stack the image to be processed and select the ROI which should be threshold.

Selection oft he ROI

Selection of the thresholding area (ROI)

Copy ROI into Clipboard via Copy

Copy of ROI into Clipboard

If the content of the clipboard is OK you can threshold it with the Threshold button

Threshold Clipboard via Threshold

Threshold Clipboard

After that the result of the threshold is shown in the clipboard window with the ROI boarder. If the result is OK you can paste the thresholded ROI from the clipboard into the target window via the Paste button. This function will only copy the black Pixels within the ROI area into the target window. White pixels will be ignored. So you can also select and place overlapping ROIs. Nevertheless you can use all the ImageJ base functions within the images or stacks.

Copy thresholded ROIs into target window via Paste

Source and target with thresholded ROIs

Finally you can save the resulting target stack by pressing the Save_Stack button. The default-name is a combination of the word Thresholded , the date and time.

Save target stack via Save_Stack

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