Extracting data from results window

[Brian Lin]

Hi all, I'm new to the ImageJ program and am trying to write a macro that
counts cells on a membrane that I have a .jpg for.
I have a macro so far that looks like this:

 dir = getDirectory("Choose a Directory ");
      list = getFileList(dir);
      setBatchMode(true);
      for (i=0; i<list.length; i++) {
          path = dir+list[i];
          open(path);
run("Make Binary");
run("Analyze Particles...", "size=35-Infinity circularity=0.7-1.00
show=Outlines display clear");
saveAs("Results", dir+i+"data.xls");
}}


Now, what this gives me is a ton of .xls files with every single spot it has
measured.
What I would love it to do is tell me only how many spots it measured in all
of the files listed by name. I assume it is possible to somehow, i dont know
parse the results page to show me the last line and output it in one large
excel spreadsheet?

Thanks for any insight anyone can provide!

--
Brian

[Krs5]

Dear Brian,

If you put the saveAs outside your for-loop it will save only at the end the table.

However, you have to make some addition changes as you seem to want a summary table and not a results table so:

dir = getDirectory("Choose a Directory ");{
list = getFileList(dir);
setBatchMode(true);
run("Set Measurements...", "  display redirect=None decimal=5");
for (i=0; i<list.length; i++) {
        path = dir+list[i];
        open(path);
        run("Make Binary");
        run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00 show=Nothing summarize");
        close();
        }
saveAs("txt", dir+i+"data.xls");
}

Hope this helps

Kees


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Brian Lin
Sent: 01 April 2011 21:03
To: [hidden email]
Subject: Extracting data from results window

Hi all, I'm new to the ImageJ program and am trying to write a macro that
counts cells on a membrane that I have a .jpg for.
I have a macro so far that looks like this:

 dir = getDirectory("Choose a Directory ");
      list = getFileList(dir);
      setBatchMode(true);
      for (i=0; i<list.length; i++) {
          path = dir+list[i];
          open(path);
run("Make Binary");
run("Analyze Particles...", "size=35-Infinity circularity=0.7-1.00
show=Outlines display clear");
saveAs("Results", dir+i+"data.xls");
}}


Now, what this gives me is a ton of .xls files with every single spot it has
measured.
What I would love it to do is tell me only how many spots it measured in all
of the files listed by name. I assume it is possible to somehow, i dont know
parse the results page to show me the last line and output it in one large
excel spreadsheet?

Thanks for any insight anyone can provide!

--
Brian

[Brian Lin]

Thanks to all of you for your assistance! They were very helpful and
definitely cut out several days of counting.
To be honest, I followed it up until Dr Straatman's suggestion. I have
absolutely no idea how it was able to summarize it all in one excel doc.
I'll try to puzzle it out myself with a bit of time.

Thanks again for all the help

Brian
--
Brian Lin
[hidden email]
[hidden email]


On Mon, Apr 4, 2011 at 5:10 AM, Straatman, Kees R. (Dr.) <
[hidden email]> wrote:

> Dear Brian,
>
> If you put the saveAs outside your for-loop it will save only at the end
> the table.
>
> However, you have to make some addition changes as you seem to want a
> summary table and not a results table so:
>
> dir = getDirectory("Choose a Directory ");{
> list = getFileList(dir);
> setBatchMode(true);
> run("Set Measurements...", "  display redirect=None decimal=5");
> for (i=0; i<list.length; i++) {
>        path = dir+list[i];
>        open(path);
>        run("Make Binary");
>         run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00
> show=Nothing summarize");
>        close();
>        }
> saveAs("txt", dir+i+"data.xls");
> }
>
> Hope this helps
>
> Kees
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Brian Lin
> Sent: 01 April 2011 21:03
> To: [hidden email]
> Subject: Extracting data from results window
>
> Hi all, I'm new to the ImageJ program and am trying to write a macro that
> counts cells on a membrane that I have a .jpg for.
> I have a macro so far that looks like this:
>
>  dir = getDirectory("Choose a Directory ");
>      list = getFileList(dir);
>      setBatchMode(true);
>      for (i=0; i<list.length; i++) {
>          path = dir+list[i];
>          open(path);
> run("Make Binary");
> run("Analyze Particles...", "size=35-Infinity circularity=0.7-1.00
> show=Outlines display clear");
> saveAs("Results", dir+i+"data.xls");
> }}
>
>
> Now, what this gives me is a ton of .xls files with every single spot it
> has
> measured.
> What I would love it to do is tell me only how many spots it measured in
> all
> of the files listed by name. I assume it is possible to somehow, i dont
> know
> parse the results page to show me the last line and output it in one large
> excel spreadsheet?
>
> Thanks for any insight anyone can provide!
>
> --
> Brian
>