Specify Multiple ROI W/ xy coordinates

[dparrell]

Hi Everyone! I have been looking for a bit and can't find a solution for part of my workflow yet. I would like to define several 3x3 pixel ROIs on an image in a similar way to the specify ROI plugin under Edit->selection, but in a more high throughput manner. I am using find maxima to identify many foci of interest in a time series stack I am using for stepwise photobleaching. I am using the macro at the end of this post to export the xy coordinates of these points to the data table.

I do not want to enter each ROI by hand if I don't need to, since there will be quite a few of them. Can anyone conceive of a way to use these xy coordinates, perhaps from an exported .csv file, to specify several ROI at once with set dimensions  i.e.. 3x3, 5x5? I guess a brute force approach would get this done in only a couple hours by hand, but I figured it is worth asking for some assistance.  Thank you for any ideas!
Daniel
---
After finding maxima I export the XY coordinates from each point with this macro. I would like to use these coordinates to place each ROI (about 50-100 per image series).

getSelectionCoordinates(xCoordinates, yCoordinates);
for(i=0; i<lengthOf(xCoordinates); i++) {
setResult("X", i, xCoordinates[i]);
setResult("Y", i, yCoordinates[i]);
}
updateResults();

[Emanuele Martini]

Only to understand better, you need something that permits you to firstly select some "Maxima/Foci points" and then create a square ROI of user definied dimension?
If yes, I have some plugins that do something similar so maybe I can help you.
Have a nice day,
Emanuele

[dparrell]

Hi Emanuele,

Yes, that is what I am looking to do. I have already designed a macro for selecting maxima using find maxima and exporting xy coordinates with the process above. So I only really need the defined dimensions ROI step, but if you have something that does all this in a different way, all at once, I'm sure that would help.

Thank you,
Daniel

[dparrell]

Hi again,
I have found a thread that does essentially what I want to do at the link below. Is this something similar to what you would suggest?
http://imagej.1557.x6.nabble.com/Add-ROIs-from-a-list-of-coordinates-in-a-CSV-file-td5009300.html

I run into a problem in the "run(specify..." line of the code referenced below. I get an error saying numerical value is expected. Here is a screen shot. Does this mean the x and Y variables are not being properly written from my cvs file? Thank you for your help!
Dan



Here is the actual code as I have edited it:

// Import it into a results table.
   run("Results... ", "open=/Users/Danny/Desktop/roi/test.csv");

for (i = 0; i < nResults; i++)
   {
      // You may need to change the "frame", etc strings to match your csv file.
      slice = getResult("f", i);
      x = getResult("x", i);
      y = getResult("y", i);

      // Using square ROI of size 10x10 pixels centered around your coordinate.
      run("Specify...", "width=10 height=10 x=&x y=&y slice=&slice centered");

      // Add to the ROI manager.
      roiManager("Add");
   }

[dparrell]

The X and Y in my CSV file were capitalized and the code was all lowercase. Once I fixed this the macro ran well. I guess my issues are solved. A little more creative searching terms brought me to the answer. Guess I should have been more persistent before posting. Thanks for the help anyhow!
-Daniel

[Straub, Volko A. (Dr.)]

It could be that the data you read from your cvs file is internally
represented as a string rather than a number.
Try using:
*parseInt(string) *(see ImageJ Macro commands)

Hope this helps,
Volko

On 18/09/2015 23:05, dparrell wrote:

> Hi again,
> I have found a thread that does essentially what I want to do at the link
> below. Is this something similar to what you would suggest?
> http://imagej.1557.x6.nabble.com/Add-ROIs-from-a-list-of-coordinates-in-a-CSV-file-td5009300.html
>
> I run into a problem in the "run(specify..." line of the code referenced
> below. I get an error saying numerical value is expected. Here is a screen
> shot. Does this mean the x and Y variables are not being properly written
> from my cvs file? Thank you for your help!
> Dan
>
> <http://imagej.1557.x6.nabble.com/file/n5014368/Screen_Shot_2015-09-18_at_6.png>
>
> Here is the actual code as I have edited it:
>
> // Import it into a results table.
>     run("Results... ", "open=/Users/Danny/Desktop/roi/test.csv");
>
> for (i = 0; i < nResults; i++)
>     {
>        // You may need to change the "frame", etc strings to match your csv
> file.
>        slice = getResult("f", i);
>        x = getResult("x", i);
>        y = getResult("y", i);
>
>        // Using square ROI of size 10x10 pixels centered around your
> coordinate.
>        run("Specify...", "width=10 height=10 x=&x y=&y slice=&slice
> centered");
>
>        // Add to the ROI manager.
>        roiManager("Add");
>     }
>
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Specify-Multiple-ROI-W-xy-coordinates-tp5014356p5014368.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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