Authors:	Bob Dougherty (rpd@optinav.com) and Wayne Rasband. Orderd by by Leila Mosavi-Maulik.
Installation:	Download MicroArray_Profile.jar to the Plugins folder and restart ImageJ.
Description:	ImageJ plugin to measure microarray image stacks. Use the control panel that appears to define the ROI (circle or rectangle) grid. This plugin uses internally controlled ROIs. Integration with the ROI management tools in ImageJ (e.g., ROI Manager...) is conceivable but not yet provided. ROIs can be moved by dragging with the mouse. Holding down the shift or alt keys while adjusting the ROI locations changes the behavior as described below. The final grid can be stored and recalled. Output to ether one text file or separate files for each ROI in the grid (single/many control). The output from "Measure files(s)", the mean gray value for each ROI, is stored in one or several files. "Measure RT" outputs to the Results Table, displaying the columns previously selected in Analyze/Set Measurements.... The Histograms button reports the histograms of all of the ROIs in the Results Table. Holding down the alt (option) key while dragging causes all of the ROIs to move together. Holding down the shift key has different effects depending on whether the ROI being dragged is a corner or an edge ROI of the grid. Shift-dragging a corner ROI causes all of the ROIs to move except the ROI that was previously adjusted. That previously adjusted ROI is a fixed point. Shift-dragging a corner ROI toward or away from the fixed point causes the grid to shrink or expand uniformly. Shift-dragging a corner ROI in an arc around the fixed point causes the grid to rotate around the fixed point. Shift-dragging a non-corner, edge ROI deforms the grid in such a way that the ROIs of the opposite edge stay fixed. Shift-dragging an edge ROI toward or away from the opposite edge produces a uni-axial compression or expansion of the grid. Shift-dragging an edge ROI parallel to the edge shears the grid. A grid can sometimes be aligned rapidly in three steps. Use the Dot Blot sample image to practice. 0. Make sure the number of rows and columns of the cicle grid matches the image. Use Reset Grid if necessary (inputs 4,7,20 for Dot Blot). 1. Alt-drag a corner ROI so that it aligns with the corresponding corner spot in the image. 2. Shift-drag an adjacent corner so that it is postioned properly. Now the whole edge connecting the two corners should be lined up with the spots. 3. Shift-drag a spot in the interior of the opposite edge until that edge is lined up with the spots. Unless the pattern of spots is distorted, all of the ROIs should now be aligned.
History:	Dec. 1, 2005 Custom ImageJ Plugin ordered Dec. 5, 2005 Version 1. Dec. 11, 2005 Version 2. Oct. 2, 2011 Version 3. Added histogram button. Oct. 3, 2011 Version 3.1 Added more columns to the histogram results table. Oct. 3, 2011 Repackaged the jar file to include Circle Arranger, which was omitted before. March 15, 2012 Added alt and shift functions for arranging circless and Results Table measurement. March 16, 2012 measure RT now pays attention to the choices in Analyze/Set Measurements.... April 13, 2012 Fixed the bug that kept the dialog from closing if the image was closed first. (Thanks to Andrew Smolak, InDevR, Inc.) April 15, 2012 Added option for rectangular ROIs.
License:	Copyright (c) 2005, 2012 OptiNav, Inc. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. Neither the name of OptiNav, Inc. nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
ImageJ:	ImageJ can be freely downloaded from the ImageJ web site.