Specify ROI

Specify ROI

Authors: Jeffrey Kuhn (jkuhn@ccwf.cc.utexas.edu)
The University of Texas at Austin
Anthony Padua (padua001@mc.duke.edu)
Duke University Medical Center, Department of Radiology

History: 2000/08/22: First version
2002/10/31: Added features
2004/08/05: Built into ImageJ 1.33i as Edit/Selection/Specify

Source: Specify_ROI.java

Installation: This plugin is built into ImageJ 1.33i or later as the Edit/Selection/Specify command.

Description: The user types in a width and height value, and the plugin create a rectangular or oval region of interest based on those values. (Why? Because it can be time-consuming to repeatedly create a ROI of an exact size with the mouse.)
Enhanced by Anthony Padua to take slice number and the option to have the x and y coordinates centered or in default top left corner of ROI.

This plugin is especially useful for speeding up the placement of ROIs of particular sizes in particular locations in an image or within a stack. (When multiple ROIs are placed, used of this plugin can be much faster than drawing or positioning these ROIs by mouse). One can further automate this process by using the macro function in ImageJ 1.29. A spreadsheet (specify-roi.xls) which has a formula for creating the macro text is availble. Spreadsheets used in this way can subsume some (but not all) of the functions of the ROI manager.
This is what the macro generated by the spreadsheet looks like:
run('Specify ROI','width=30 height=20 x=80 y=90 slice=3 oval centered')
run('Specify ROI','width=30 height=20 x=80 y=90 slice=4')
run('Specify ROI','width=30 height=20 x=80 y=90 slice=5 centered')
run('Specify ROI','width=30 height=20 x=80 y=90 slice=6 oval')
run('Specify ROI','width=30 height=20 x=80 y=90 slice=7 oval')

To use it to generate an ROI, paste it into an ImageJ text editor window (Plugins/New), select one line, then press ctrl-r.

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Authors:	Jeffrey Kuhn (jkuhn@ccwf.cc.utexas.edu) The University of Texas at Austin Anthony Padua (padua001@mc.duke.edu) Duke University Medical Center, Department of Radiology
History:	2000/08/22: First version 2002/10/31: Added features 2004/08/05: Built into ImageJ 1.33i as Edit/Selection/Specify
Source:	Specify_ROI.java
Installation:	This plugin is built into ImageJ 1.33i or later as the Edit/Selection/Specify command.
Description:	The user types in a width and height value, and the plugin create a rectangular or oval region of interest based on those values. (Why? Because it can be time-consuming to repeatedly create a ROI of an exact size with the mouse.) Enhanced by Anthony Padua to take slice number and the option to have the x and y coordinates centered or in default top left corner of ROI. This plugin is especially useful for speeding up the placement of ROIs of particular sizes in particular locations in an image or within a stack. (When multiple ROIs are placed, used of this plugin can be much faster than drawing or positioning these ROIs by mouse). One can further automate this process by using the macro function in ImageJ 1.29. A spreadsheet (specify-roi.xls) which has a formula for creating the macro text is availble. Spreadsheets used in this way can subsume some (but not all) of the functions of the ROI manager. This is what the macro generated by the spreadsheet looks like: run('Specify ROI','width=30 height=20 x=80 y=90 slice=3 oval centered') run('Specify ROI','width=30 height=20 x=80 y=90 slice=4') run('Specify ROI','width=30 height=20 x=80 y=90 slice=5 centered') run('Specify ROI','width=30 height=20 x=80 y=90 slice=6 oval') run('Specify ROI','width=30 height=20 x=80 y=90 slice=7 oval') To use it to generate an ROI, paste it into an ImageJ text editor window (Plugins/New), select one line, then press ctrl-r.