Help with particle analysis filter

[Eric Casavant]

Hi,
I am trying to use ImageJ to find a few hundred "particles" on a
picture. However, I found it best to filter the particles found with
imageJ through excel filters. So, I was wondering if it was possible
to then develop an outline of only the particles that passed the excel
filter on imageJ (not the ones that the "analyze particles" search
found). What would be really convenient is if I could make a mask of
those particles which could then be placed over the original image.

Thanks,
Eric

[Marcel]

What about selections with an opened ROI Manager ("Add to Manager" option)?
You can create an array with your particles and then select them in the ROI Manager.

Here a short snippet for a plugin which have to be filled with your methods etc.:

public class Select_ implements PlugIn {
 /*Example selection as an array!*/
int [] selection={1,5,8,12};
       
        public void run(String arg) {
        if (RoiManager.getInstance() != null) {
           RoiManager roiManager=RoiManager.getInstance();
               for(int i=0;i<selection.length;i++){
              /*Select more than one particle in the ROI Manager!*/
               roiManager.select(selection[i]-1,true,false);
               }
            }
        }

}

With kind regards

M.Austenfeld

[Sami Badawi-2]

Hi Eric,

Here is an idea that might work:
Run particle analyzer
Export to Excel
Run your Excel filter
Write out filtered result to a csv file
Write a macro or a plugin that for each csv line reads the start x,y
coordinates and do a flood fill to the background color from each start
point

-Sami Badawi
http://www.shapelogic.org

On Thu, Aug 7, 2008 at 12:15 PM, Eric Casavant <[hidden email]>wrote:

> Hi,
> I am trying to use ImageJ to find a few hundred "particles" on a
> picture. However, I found it best to filter the particles found with
> imageJ through excel filters. So, I was wondering if it was possible
> to then develop an outline of only the particles that passed the excel
> filter on imageJ (not the ones that the "analyze particles" search
> found). What would be really convenient is if I could make a mask of
> those particles which could then be placed over the original image.
>
> Thanks,
> Eric
>