differences in integrated densities

[Karen Kempler]

  I have a problem with integrated density numbers.  I have a 75 fold difference in integrated
densities of an image depending on whether we analyze it in Image J or with the SP2 or SP5 Leica software.  We don't understand where this difference is coming from.  The areas are the same, but the densities within these areas are 75 fold less with Image J.  The problem is that we want to compile data that has already been analyzed with the SP2 software with data we are now analyzing with Image J.  Does anyone have any idea why this is?  Thank you.

[vischer]

Hi Karen,
I also had this problem until I realized that in ImageJ's equation
        IntDens=area * mean
area is scaled (e.g in square microns). Many other packages use pixel count for area. The advantage in ImageJ is that you don't get those large numbers. Personally I would have preferred the non-scaled version; when solving image processing problems, I usually think in pixels and not in microns.

regards, Norbert



>
> I have a problem with integrated density numbers.  I have a 75 fold difference in integrated
> densities of an image depending on whether we analyze it in Image J or with the SP2 or SP5 Leica software. We don't understand where this difference is coming from.  The areas are the same, but the densities within these areas are 75 fold less with Image J.  The problem is that we want to compile data that has already been analyzed with the SP2 software with data we are now analyzing with Image J.  Does anyone have any idea why this is?  Thank you.

[Glen MacDonald-2]

Are both sets of files being saved and opened at the same bit-depth?  

Glen

Glen MacDonald
Core for Communication Research
Virginia Merrill Bloedel Hearing Research Center
Box 357923
University of Washington
Seattle, WA 98195-7923  USA
[phone]
[hidden email]








On Jan 22, 2010, at 11:44 AM, Karen Kempler wrote:

> I have a problem with integrated density numbers.  I have a 75 fold difference in integrated
> densities of an image depending on whether we analyze it in Image J or with the SP2 or SP5 Leica software.  We don't understand where this difference is coming from.  The areas are the same, but the densities within these areas are 75 fold less with Image J.  The problem is that we want to compile data that has already been analyzed with the SP2 software with data we are now analyzing with Image J.  Does anyone have any idea why this is?  Thank you.

[Gabriel Landini]

On Friday 22 January 2010, you wrote:
> Hi Karen,
> I also had this problem until I realized that in ImageJ's equation
> IntDens=area * mean
> area is scaled (e.g in square microns). Many other packages use pixel count
>  for area. The advantage in ImageJ is that you don't get those large
>  numbers. Personally I would have preferred the non-scaled version; when
>  solving image processing problems, I usually think in pixels and not in
>  microns.

Doesn't this return the ID in pixels if the image is not calibrated?
Running something like:
run("Properties...", "unit=pixel pixel_width=1 pixel_height=1 voxel_depth=1");
before the particle analyzer would do.

BTW, the partilces8 plugin computes the ID in pixel calibration.

Cheers

G.