Saving the ROI in JPEG....

[Madhoosudan]

Hi I am working on the image where I am assigning the efferent ROI to
measure it. After I am done with this I want to save the image along with
selected ROI which can be opened in any image viewing application. I tried
saving the image as tiff. But in that case I can only see the ROI if I
reopen the image in ImageJ but not in any other default widows applications.

--
​
​Regards,


​Madhoosudan Patil,
Post Doctoral Fellow,
​Skaggs School of Pharmacy,​

​Anschutz Medical Campus,​
​University of Colorado, Denver, USA.
​Ph.: 001 [phone]
E-Mail: [hidden email]

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[CARL Philippe (LBP)]

Dear Patil,
To my knowledge (but I may be wrong) you won't have overlay or ROI features within a JPEG picture.
What you can do in ImageJ is to put the ROI(s) within the ROI Manager and then save this(ese) ROI(s) within a separate file (More->Save... in the ROI Manager window).
Alternativelly, if you want to see ROI(s) within other softwares you can just draw them (Edit->Draw or Ctrl + D) on the given picture with the color defined as the foreground one and a width defined in Edit->Options->Line_width...
But in this case you will be loosing all the ROI(s) functionalities...

My best regards,
Philippe

Le Vendredi 19 Août 2016 17:24 CEST, madhoosudan patil <[hidden email]> a écrit:

> Hi I am working on the image where I am assigning the efferent ROI to> measure it. After I am done with this I want to save the image along with
> selected ROI which can be opened in any image viewing application. I tried
> saving the image as tiff. But in that case I can only see the ROI if I
> reopen the image in ImageJ but not in any other default widows applications.
>
> --
> ​
> ​Regards,
>
>
> ​Madhoosudan Patil,
> Post Doctoral Fellow,
> ​Skaggs School of Pharmacy,​
>
> ​Anschutz Medical Campus,​
> ​University of Colorado, Denver, USA.
> ​Ph.: 001 [phone]
> E-Mail: [hidden email]
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ctrueden]

Hi Madhoosudan,

It is possible to embed ROIs into a saved TIFF.

After adding your ROIs to the ROI manager, clear the selection and then run:

Image > Overlay > From ROI Manager

Then save as TIFF.

When you reopen this TIFF, the ROIs will come back in as an overlay. You
can then restore them to the ROI Manager for individual processing using:

Image > Overlay > To ROI Manager

Maybe someone knows an easier way, but this approach should work.

However, note that when testing this feature, I noticed a bug where the
hyperstack position of ROIs might be altered in some circumstances. I filed
an bug report: https://github.com/imagej/imagej1/issues/21.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - http://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Fri, Aug 19, 2016 at 10:24 AM, madhoosudan patil <
[hidden email]> wrote:

> Hi I am working on the image where I am assigning the efferent ROI to
> measure it. After I am done with this I want to save the image along with
> selected ROI which can be opened in any image viewing application. I tried
> saving the image as tiff. But in that case I can only see the ROI if I
> reopen the image in ImageJ but not in any other default widows
> applications.
>
> --
> ​
> ​Regards,
>
>
> ​Madhoosudan Patil,
> Post Doctoral Fellow,
> ​Skaggs School of Pharmacy,​
>
> ​Anschutz Medical Campus,​
> ​University of Colorado, Denver, USA.
> ​Ph.: 001 [phone]
> E-Mail: [hidden email]
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Michael Schmid]

Hi ​Madhoosudan,

if you save an image as PNG or JPG, ImageJ puts overlays into the image
data. You can then see these overlays in any image viewer, but you
cannot recover the original image behind them.
Use Image>Overlay>Add Selection to convert a ROI into an overlay.
For multiple ROIs in the ROI Manager, you can use Image>Overlay>From ROI
Manager.

JPG has the disadvantage that it is a lossy compression; especially the
1-pixel wide ROI boundaries often look awful. Better use PNG.

If you save an image as TIFF, ImageJ saves the ROI boundaries and
overlays into private fields of the TIFF file, and the image data remain
unchanged. If you have the ROI manager open, with several ROIs visible,
ImageJ stores all of them (e.g. for later analysis).
There is no general standard how to save ROIs in a TIFF file, so there
is no way to make the ROIs accessible as ROIs to other software.
Also, other software would not support all ROI types of ImageJ.

The advantage of the TIFF format is that it preserves the original image
data (and ROIS, overlays, metadata...) for further analysis in ImageJ.


Michael
________________________________________________________________

On 2016-08-19 17:24, madhoosudan patil wrote:

> Hi I am working on the image where I am assigning the efferent ROI to
> measure it. After I am done with this I want to save the image along with
> selected ROI which can be opened in any image viewing application. I tried
> saving the image as tiff. But in that case I can only see the ROI if I
> reopen the image in ImageJ but not in any other default widows applications.
>
> --
> ​
> ​Regards,
>
>
> ​Madhoosudan Patil,
> Post Doctoral Fellow,
> ​Skaggs School of Pharmacy,​
>
> ​Anschutz Medical Campus,​
> ​University of Colorado, Denver, USA.
> ​Ph.: 001 [phone]
> E-Mail: [hidden email]
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html