Re: Saving single ROI as jpg

Posted by Douglas Benn-2 on Apr 10, 2010; 9:27pm
URL: http://imagej.273.s1.nabble.com/Saving-single-ROI-as-jpg-tp3688628p3688630.html

Dear Michael,

Thank you for your reply.

I did as you suggested and it saved a jpg but the region recorded by selecting the ROI in the manager was a clipped ROI outline as in Drawing 07-1a.jpg  . By manually selecting a rectangular region around the ROI which was larger than the ROI I recorded the whole ROI as in Drawing 07-1.jpg

It looks like the containing box of the ROI is cutting off the outline by 1x and 1y. I suppose I could generate the box width & height in the Results table and increase that +1x and +1y to ensure my ROI is not cropped.

Thanks for your help.

Douglas

Dr Douglas K Benn, BDS, M.Phil., Ph.D., Dipl. Dental Radiology (Royal College of Radiologists, England).
Professor
Dept of General Dentistry
Creighton University Dental School
2500 California Plaza
Omaha
Nebraska 68178

Tel: [phone]
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-----Original Message-----
From: ImageJ Interest Group on behalf of Michael Doube
Sent: Sat 4/10/2010 1:46 PM
To: [hidden email]
Subject: Re: Saving single ROI as jpg
 
Douglas

You can duplicate the image data inside the ROI, then save as JPG and
close. Image>Duplicate, File>Save As>JPG, File>Close.

This is the macro code of this sequence of commands:

run("Duplicate...");
saveAs("Jpeg");
close();

For a set of ROIs from an ROI manager, you could do it like:

 n = roiManager("count");
 for (i=0; i<n; i++) {
        roiManager("select", i);
        run("Duplicate...");
        saveAs("Jpeg");
        close();
  }

This could be streamlined to set filenames automatically, and would be
faster in batch mode, if you have a lot of images / ROI's to save.

http://rsbweb.nih.gov/ij/developer/macro/functions.html

Michael


Benn, Douglas K. wrote:

> Once again some advice please. I am trying to select individual ROIs and save them as jpgs. My process is
>
> 1) input stack 16 bits images.
> 2) threshold with black background.
> 3) apply a mask.
> 4) extract outlines.
> 4) analyse with output as drawing of ROIs with object labels shown. The ROImanager is enabled.
>
> I have been able to save individual rois as .roi and retrieve them to display on an image. However, I cannot find a way to select a region and save this as a jpg. Any suggestions would be appreciated.
>
> Thanks.
>
> Douglas