Outline selection in one channel, display in another

Hello all: this has to be a simple process but I can’t figure it out. We have multichannel fluorescent images for which we would like to be able to visualize whether, for instance, a green cell is also red, by drawing a green outline around all the green cells and displaying it on the red channel. In this example, we would want the entire red image to remain visible, so I don’t think a green mask will work (although there are probably mask options I don’t know about). The way I used to do this in Canvas for Mac (which is now a shell of its former self) was by using the wand selection tool to select (in the above example) the green areas of interest, then converting the selection to a path, coloring the path green, and placing it on the red channel. I can’t figure out how to do this in ImageJ, although I suspect this is also possible, but any method that works would be fine.

Thank you for your help!

Hello there,
So if i am right you need to show the ROI in both your channels? I would first use the ‘Polygon selection tool’ on the green channel to mark the region. You may also change the color of this line under ‘Edit>>Options>>Color’. Once you have made your selection switch to the red channel and ‘restore’ the selection you just made on this channel. You can do this again by Edit>>Restore Selection. Now if you want to flatten this selection on your red channel add your selection to the 'ROI manager ’ (Edit>>Selection>>Add to manger) and then use the ‘flatten’ option in ROI manager. Hope this helps.


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Hi Praveen: thanks for your response! That does help, but using the polygon selection tool (or any other hand-drawn shape) will take too long for some of our more complex tissues. What I would like to do, for instance, is to select all the areas within a given color range (whether continuous or discontinuous) and then draw the colored border around these. Let me know if you have any ideas. thanks again! howard

You can use Image > Adjust > Threshold (Shift-T) on your green channel, then Edit > Selection > Create Selection and restore this on the red channel with Shift-E.

Here’s a macro I just recorded to illustrate this:

run("Fluorescent Cells (400K)");
run("Split Channels"); // Image > Color > Split Channels
setAutoThreshold("Default dark"); // Shift-T
run("Create Selection"); // Edit > Selection > Create Selection
run("Restore Selection"); // Shift-E
run("Colors...", "foreground=white background=black selection=blue"); // Edit > Options > Colors...

The same works with the Wand tool. To manage several selections, use the ROI manager as @Praveen suggests.

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Yes! That’s pretty good! let me play with parameters and see how it goes. Thanks to both of you!