If the selection within the scatterPlot is deleted (for example with a by a single clic outside of the graph within the scatterplot window), it is automatically regenerated to its initial settings (i.e.max2: the higher intensity value of the second picture defined by the ROI, this value will be set to the maximal intensity value of the second picture in the case the set value is a whatever String.min2: the lower intensity value of the second picture defined by the ROI, this value will be set to the minimal intensity value of the second picture in the case the set value is a whatever String.
![colocalization imagej software colocalization imagej software](https://media.springernature.com/lw685/springer-static/image/art%3A10.1038%2Fs41598-018-33592-8/MediaObjects/41598_2018_33592_Fig2_HTML.png)
max1: the higher intensity value of the first picture defined by the ROI, this value will be set to the maximal intensity value of the first picture in the case the set value is a whatever String.min1: the lower intensity value of the first picture defined by the ROI, this value will be set to the minimal intensity value of the first picture in the case the set value is a whatever String (for exemple '' or "").'call("Colocalization_tScatterPlotRoi", min1, max1, min2, max2) ' The limits within the scatterPlot selection can as well be defined by using the macro instruction:.The selection within the scatterPlot can also be set through a dialog box opened either by the "Set" button (at the bottom left of the scatterPlot picture) or the 'g' key.Drawing or modifying a selection within the scatterPlot (which limit values will be shown within a label panel at the bottom of the scatterPlot picture) allows to highlight the corresponding pixels within the composite picture.The user interface of the plugin provides the following features:
![colocalization imagej software colocalization imagej software](https://i.ytimg.com/vi/jNYahr81x30/maxresdefault.jpg)
The initial scatterPlot plot limits correspond to the minimal and maximal intensity values of the input pictures. This plugin displays a correlation diagram (called scatterPlot picture) from two initial pictures having the same size together with a RGB overlap of the original images (called Composite picture). To open a JAR file, change the extension from ".jar" to ".zip" and double click on it.ĭownload Colocalization_Finder.jar to the plugins folder, or subfolder, restart ImageJ, and there will the " Colocalization Finder." new command in the Plugins menu. the possibility to set ROIs with given colors with a mouse double click has been erased (due to the ImageJ 1.53c 26 June 2020 update) and replaced by a Ctrl + mouse click user actionĬontained in the JAR file. addition of a "Set" button at the bottom left of the scatterPlot picture allowing so set the limits of the scatterPlot graph and/or of the scatterPlot Roi (the 'g' key gives the same features) addition of a label panel at the bottom of the scatterPlot picture displaying the limits of the scatterPlot Roi selection possibility to choose the size of the scatter plot upon start of the plugin addition of synchronized background thread for smoothly updating the calculations on the fly possibility to add a selection within the Composite picture to restric the analysis to a given selection the colocalization calculations are performed using double parameters instead of float
![colocalization imagej software colocalization imagej software](https://ars.els-cdn.com/content/image/1-s2.0-S1046202316304649-gr1.jpg)
addition of scripting possibilities illustrated within the macro examples that can be downloaded here and here. possibility to generate the x or y histogram with a Gaussian fit in order to extract the histogram maximum position by using the numeric pad 4/6 or 2/8 keys possibility to set ROIs with given colors with a mouse double click
![colocalization imagej software colocalization imagej software](https://imagej.net/media/imaging/coloctestgui2.png)
possibility to move the ROI position (within the scatter plot) from the mouse position within the overlay picture the selected points within the overlay picture are updated as soon as the ROI in the scatter plot is modified or dragged over addition of a plot (with legends, ticks (minor and major), labels) within the scatter plot extension of the plugin for whatever picture dynamics replacement of the deprecated functions (getBoundingRect, IJ.write) by the new ones
COLOCALIZATION IMAGEJ SOFTWARE UPDATE
You now have to click in the ROI to update overaly image(s) and statistics Chinga.Ĩ: Version 1.1: statistical methods added.
COLOCALIZATION IMAGEJ SOFTWARE CODE
Philippe Carl (maintainer), UMR7021, Strasbourg, France.Ģ: First version: parts of the initial code were taken from plugins by W. Jerome Mutterer, Institut de Biologie Moleculaire des Plantes, Strasbourg, France. Colocalization_Finder Colocalization_Finder