Hi Andrew,
two options:
(1) If you don't care about the sequence, simply remove the first
line from your macro and run it with the thresholded image.
(2) If you want the particles (bacteria) in the proper sequence, use
'add to roi manager' on the particle analyzer and loop over the rois.
Michael
________________________________________________________________
On 17 Sep 2009, at 11:03, Andrew Bell wrote:
> Dear All,
>
> I am trying to find a way to list all pixel values for a given ROI.
> Having
> searched the archive, I found a code that gives the pixel values for a
> predetermined roi.
>
> getSelectionBounds(xmin, ymin, selwidth, selheight);
> run("Create Mask");
> m=newArray(w*h);
> for(x=0;x<w;x++){
> for(y=0;y<h;y++){
> m[y*w+x]=getPixel(x,y);
> }
> }
> close(); //close mask
> for(x=xmin;(x<=xmin+selwidth);x++){
> for(y=ymin;(y<=ymin+selheight);y++){
> if (m[y*w+x]!=0) print (x,y,getPixel(x,y));
> }
> }
>
> What I have are images with up to 50 bacterial cells, and having
> thresholded the image, I would like a list of the pixel values for
> each
> ROI. I know in principle how to do this for a single ROI in turn,
> but with
> approx 1200 cells that would take a long time. Is there a way to do
> this?
> Or will I have to do it by hand as it were?
>
> Regards,
>
> Andrew
Locked
