Saving single ROI as jpg

[Douglas Benn-2]

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

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]
Fax: [phone]

[Michael Doube]

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

[Douglas Benn-2]

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]
Fax: [phone]



-----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

[Michael Schmid]

Hi Douglas,

maybe the problem is due to the way ROIs are drawn in Image?

The boundary line (usually yellow unless you have changed the color) is
inside the roi on the upper and left sides, but outside the roi on the
bottom and right sides. It is the same for the line created by Edit>Draw
and the Outlines created by Analyze Particles.

By the way, this also means that there won't be an outline if the roi
touches the edge of the image at the bottom or right side.

Michael
_________________________________________________________________________

On Sat, April 10, 2010 23:27, Benn, Douglas K. wrote:

> 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]
> Fax: [phone]
>
>
>
> -----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
>
>
>