macro ImageJ

[Nascimbeni]

Hello all,

We do have a macro "Analyze Particles" (the copy is joined below).
We would like to add to that macro a watershed function.
We tried to add run("Watershed"); just after setThreshold(30, 80); but
this did not work. A message telling "8-bit binary image (0 and 255)  
required" appears.
Anybody has a solution???

Thanks a lot
Best regards
Michelina Nascimbeni



requires("1.38o");
     dir = getDirectory("Choose a Directory ");
     list = getFileList(dir);
     setBatchMode(true);
     for (i=0; i<list.length; i++) {
         showProgress(i, list.length);
         open(dir+list[i]);
         getStatistics(area, mean, min, max, std);
         threshold = mean + 2.5*std;
         setThreshold(30, 80);
         run("Analyze Particles...", "size=100-650 summarize");
         close;
     }
     selectWindow("Summary");
     saveAs("Text", getDirectory("home")+"Summary.txt");

[Michael Schmid]

Hi Michelina,

you have to run Edit>Selection>Create Mask after setThreshold:
   run("Create Mask");
This creates the 8-bit binary image required.
The mask will be in a separate window, so don't forget to close
both, the mask and the original window.

Michael
________________________________________________________________

On 11 Jul 2007, at 16:35, Nascimbeni wrote:

> Hello all,
>
> We do have a macro "Analyze Particles" (the copy is joined below).
> We would like to add to that macro a watershed function.
> We tried to add run("Watershed"); just after setThreshold(30, 80); but
> this did not work. A message telling "8-bit binary image (0 and 255)
> required" appears.
> Anybody has a solution???
>
> Thanks a lot
> Best regards
> Michelina Nascimbeni
>
>
>
> requires("1.38o");
>      dir = getDirectory("Choose a Directory ");
>      list = getFileList(dir);
>      setBatchMode(true);
>      for (i=0; i<list.length; i++) {
>          showProgress(i, list.length);
>          open(dir+list[i]);
>          getStatistics(area, mean, min, max, std);
>          threshold = mean + 2.5*std;
>          setThreshold(30, 80);
>          run("Analyze Particles...", "size=100-650 summarize");
>          close;
>      }
>      selectWindow("Summary");
>      saveAs("Text", getDirectory("home")+"Summary.txt");

[Michelina Nascimbeni]

Hi Michael,

Thanks for your answer. Actually, our macro runs on a folder containing a
set of images. We need to include the watershed function into this macro and
run this on the whole folder not only on one single picture.
Any other idea?
Thanks
Michelina


2007/7/11, Michael Schmid <[hidden email]>:

>
> Hi Michelina,
>
> you have to run Edit>Selection>Create Mask after setThreshold:
>    run("Create Mask");
> This creates the 8-bit binary image required.
> The mask will be in a separate window, so don't forget to close
> both, the mask and the original window.
>
> Michael
> ________________________________________________________________
>
> On 11 Jul 2007, at 16:35, Nascimbeni wrote:
>
> > Hello all,
> >
> > We do have a macro "Analyze Particles" (the copy is joined below).
> > We would like to add to that macro a watershed function.
> > We tried to add run("Watershed"); just after setThreshold(30, 80); but
> > this did not work. A message telling "8-bit binary image (0 and 255)
> > required" appears.
> > Anybody has a solution???
> >
> > Thanks a lot
> > Best regards
> > Michelina Nascimbeni
> >
> >
> >
> > requires("1.38o");
> >      dir = getDirectory("Choose a Directory ");
> >      list = getFileList(dir);
> >      setBatchMode(true);
> >      for (i=0; i<list.length; i++) {
> >          showProgress(i, list.length);
> >          open(dir+list[i]);
> >          getStatistics(area, mean, min, max, std);
> >          threshold = mean + 2.5*std;
> >          setThreshold(30, 80);
> >          run("Analyze Particles...", "size=100-650 summarize");
> >          close;
> >      }
> >      selectWindow("Summary");
> >      saveAs("Text", getDirectory("home")+"Summary.txt");
>

[Michael Schmid]

Hi Michelina,

no problem, you have to put it into the loop of your macro.

requires("1.38o");
       dir = getDirectory("Choose a Directory ");
       list = getFileList(dir);
       setBatchMode(true);
       for (i=0; i<list.length; i++) {
           showProgress(i, list.length);
           open(dir+list[i]);
           getStatistics(area, mean, min, max, std);
           threshold = mean + 2.5*std;
           setThreshold(30, 80);
//probably you want something like setThreshold(threshold, max); here?
           run("Create Mask");
           rename(list[i]); //otherwise all lines in the summary will  
be labelled "mask"
           run("Watershed");
           run("Analyze Particles...", "size=100-650 summarize");
           close;
           close;
       }
       selectWindow("Summary");
       saveAs("Text", getDirectory("home")+"Summary.txt");


Michael
________________________________________________________________

On 11 Jul 2007, at 17:50, Michelina Nascimbeni wrote:

> Hi Michael,
>
> Thanks for your answer. Actually, our macro runs on a folder  
> containing a
> set of images. We need to include the watershed function into this  
> macro and
> run this on the whole folder not only on one single picture.
> Any other idea?
> Thanks
> Michelina

[Michelina Nascimbeni]

Thanks a lot Michael. This works fine!
Michelina

2007/7/12, Michael Schmid <[hidden email]>:

>
> Hi Michelina,
>
> no problem, you have to put it into the loop of your macro.
>
> requires("1.38o");
>        dir = getDirectory("Choose a Directory ");
>        list = getFileList(dir);
>        setBatchMode(true);
>        for (i=0; i<list.length; i++) {
>            showProgress(i, list.length);
>            open(dir+list[i]);
>            getStatistics(area, mean, min, max, std);
>            threshold = mean + 2.5*std;
>            setThreshold(30, 80);
> //probably you want something like setThreshold(threshold, max); here?
>            run("Create Mask");
>            rename(list[i]); //otherwise all lines in the summary will
> be labelled "mask"
>            run("Watershed");
>            run("Analyze Particles...", "size=100-650 summarize");
>            close;
>            close;
>        }
>        selectWindow("Summary");
>        saveAs("Text", getDirectory("home")+"Summary.txt");
>
>
> Michael
> ________________________________________________________________
>
> On 11 Jul 2007, at 17:50, Michelina Nascimbeni wrote:
>
> > Hi Michael,
> >
> > Thanks for your answer. Actually, our macro runs on a folder
> > containing a
> > set of images. We need to include the watershed function into this
> > macro and
> > run this on the whole folder not only on one single picture.
> > Any other idea?
> > Thanks
> > Michelina
>