cannot save summary file in macro

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cannot save summary file in macro

atyagiaa
Hi,

Please help in making following code work to save summary that involve cell
count, the macro code as follows:

I have many images of cells, i want to count cell number for cells in
different images, the problem here is
1. I can see the summary display for individual file name, but that can not
save in one slice of summary file, please suggest what to do. I want to
compile all to one file so that i can save them as excel file.
<http://imagej.1557.x6.nabble.com/file/t381858/first-window.png>
2. I can save results easily as summary. the following file can be saved
easily.
<http://imagej.1557.x6.nabble.com/file/t381858/second-window.jpg>

The code is as follows:

run("Subtract Background...", "rolling=12 light");
setAutoThreshold("Default");
//run("Threshold...");
setOption("BlackBackground", false);
run("Convert to Mask");
run("Close");
run("Fill Holes");
run("Watershed");
run("Convert to Mask");
run("Analyze Particles...", "size=200-Infinity show=Outlines display clear
include summarize add");
run("Close");
selectWindow("Results");
saveAs("Results", homedir + File.separator +  "summary.csv");
close();

Please suggest the solution for this problem
Thanks in advance

Abhi



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Re: cannot save summary file in macro

Herbie
This is a cross-post from the IJ-forum:
<http://forum.imagej.net/t/cannot-save-macro-images/8235?u=herbie>


Am 11.12.17 um 19:08 schrieb atyagiaa:

> Hi,
>
> Please help in making following code work to save summary that involve cell
> count, the macro code as follows:
>
> I have many images of cells, i want to count cell number for cells in
> different images, the problem here is
> 1. I can see the summary display for individual file name, but that can not
> save in one slice of summary file, please suggest what to do. I want to
> compile all to one file so that i can save them as excel file.
> <http://imagej.1557.x6.nabble.com/file/t381858/first-window.png>
> 2. I can save results easily as summary. the following file can be saved
> easily.
> <http://imagej.1557.x6.nabble.com/file/t381858/second-window.jpg>
>
> The code is as follows:
>
> run("Subtract Background...", "rolling=12 light");
> setAutoThreshold("Default");
> //run("Threshold...");
> setOption("BlackBackground", false);
> run("Convert to Mask");
> run("Close");
> run("Fill Holes");
> run("Watershed");
> run("Convert to Mask");
> run("Analyze Particles...", "size=200-Infinity show=Outlines display clear
> include summarize add");
> run("Close");
> selectWindow("Results");
> saveAs("Results", homedir + File.separator +  "summary.csv");
> close();
>
> Please suggest the solution for this problem
> Thanks in advance
>
> Abhi
>
>
>
> --
> Sent from: http://imagej.1557.x6.nabble.com/
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: cannot save summary file in macro

Straatman, Kees (Dr.)
In reply to this post by atyagiaa
Dear Abhi,

To save a summary file you have to select it before you can save it.

selectWindow("Summary");
saveAs("Summary", homedir + File.separator +  "summary.csv");

(if you want to close the selected table after saving it you need run("Close");)

Best wishes

Kees


Dr Ir K.R. Straatman
Senior Experimental Officer
Advanced Imaging Facility
Centre for Core Biotechnology Services
University of Leicester
www.le.ac.uk/advanced-imaging-facility


-----Original Message-----
From: atyagiaa [mailto:[hidden email]]
Sent: 11 December 2017 18:08
To: [hidden email]
Subject: cannot save summary file in macro

Hi,

Please help in making following code work to save summary that involve cell count, the macro code as follows:

I have many images of cells, i want to count cell number for cells in different images, the problem here is 1. I can see the summary display for individual file name, but that can not save in one slice of summary file, please suggest what to do. I want to compile all to one file so that i can save them as excel file.
<http://imagej.1557.x6.nabble.com/file/t381858/first-window.png>
2. I can save results easily as summary. the following file can be saved easily.
<http://imagej.1557.x6.nabble.com/file/t381858/second-window.jpg>

The code is as follows:

run("Subtract Background...", "rolling=12 light"); setAutoThreshold("Default"); //run("Threshold..."); setOption("BlackBackground", false); run("Convert to Mask"); run("Close"); run("Fill Holes"); run("Watershed"); run("Convert to Mask"); run("Analyze Particles...", "size=200-Infinity show=Outlines display clear include summarize add"); run("Close"); selectWindow("Results"); saveAs("Results", homedir + File.separator +  "summary.csv"); close();

Please suggest the solution for this problem Thanks in advance

Abhi



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