Summing areas within larger areas

[Darren Johnson]

Hello all,

I have only been using ImageJ for a couple of weeks but have found it very useful in my research. I am looking for a way to sum smaller areas that reside in larger areas. For example, I have an image showing several hundred grains that I have done particle analysis on and therefore have the outlines (and areas) of each of the individual grains. I also have an image that shows iron bearing minerals within these grains. I have done a separate particle analysis on the iron bearing image and also have the outlines for them. I was wondering if there is a way to use the separate outline images to sum all of the small areas (iron bearing minerals) that lie within the boundaries of larger areas (i.e. each individual grain). An added bonus would be if I could retain the original numbers associated with individual grain image, although this is not as important. It is virtually impossible to manually do this because some of the grains may have 40 to 50 Fe bearing minerals (small areas) so the numbers overlap and are difficult to distinguish.


Thanks,
 
Darren Johnson
Washington University in St. Louis

[Stephan Saalfeld]

Hi Luciano,
       
to some extent it depends on how big your largest factor actually is.
As long as it is smaller than 255, you are fine with 8bit after dividing
by 1023.  Then you could save the images as GIF.  Typically, PNG is the
best choice for 8bit greyscale or 24bit rgb images with large
homogeneous regions, but I noticed some unexpected contrast changes
during my last attempts with ImageJ's PNG export.

Best regards,
Stephan


On Tue, 2008-08-12 at 11:27 -0600, Darren Johnson wrote:
> Hello all,
>
> I have only been using ImageJ for a couple of weeks but have found it very useful in my research. I am looking for a way to sum smaller areas that reside in larger areas. For example, I have an image showing several hundred grains that I have done particle analysis on and therefore have the outlines (and areas) of each of the individual grains. I also have an image that shows iron bearing minerals within these grains. I have done a separate particle analysis on the iron bearing image and also have the outlines for them. I was wondering if there is a way to use the separate outline images to sum all of the small areas (iron bearing minerals) that lie within the boundaries of larger areas (i.e. each individual grain). An added bonus would be if I could retain the original numbers associated with individual grain image, although this is not as important. It is virtually impossible to manually do this because some of the grains may have 40 to 50 Fe bearing minerals (small areas) so the numbers overlap and are difficult to distinguish.
>
>
> Thanks,
>  
> Darren Johnson
> Washington University in St. Louis

[Stephan Saalfeld]

Sorry for that misplaced answer.  The ImageJ-mailing list rejects signed
mails such that I had to resend my answer to Luciano Marpegan.
Obviously I did something wrong during this attempt.

Best regards,
Stephan
       

On Tue, 2008-08-12 at 20:59 +0200, Stephan Saalfeld wrote:

> Hi Luciano,
>        
> to some extent it depends on how big your largest factor actually is.
> As long as it is smaller than 255, you are fine with 8bit after
> dividing
> by 1023.  Then you could save the images as GIF.  Typically, PNG is
> the
> best choice for 8bit greyscale or 24bit rgb images with large
> homogeneous regions, but I noticed some unexpected contrast changes
> during my last attempts with ImageJ's PNG export.
>
> Best regards,
> Stephan
>
>
> On Tue, 2008-08-12 at 11:27 -0600, Darren Johnson wrote:
> > Hello all,
> >
> > I have only been using ImageJ for a couple of weeks but have found
> it very useful in my research. I am looking for a way to sum smaller
> areas that reside in larger areas. For example, I have an image
> showing several hundred grains that I have done particle analysis on
> and therefore have the outlines (and areas) of each of the individual
> grains. I also have an image that shows iron bearing minerals within
> these grains. I have done a separate particle analysis on the iron
> bearing image and also have the outlines for them. I was wondering if
> there is a way to use the separate outline images to sum all of the
> small areas (iron bearing minerals) that lie within the boundaries of
> larger areas (i.e. each individual grain). An added bonus would be if
> I could retain the original numbers associated with individual grain
> image, although this is not as important. It is virtually impossible
> to manually do this because some of the grains may have 40 to 50 Fe
> bearing minerals (small areas) so the numbers overlap and are
> difficult to distinguish.
> >
> >
> > Thanks,
> >  
> > Darren Johnson
> > Washington University in St. Louis