Selecting specific slice from the summary table

[aw29]

Hi!

I'm currently working on code that will allow me to threshold and analyze
two channels (1 and 2) for multiple images. The first channel works
perfectly, but the second one is having trouble transferring data to my
excel spreadsheet because of the "Process Stack?" pop-up window. After I go
through and do all of the thresholding and analysis, I get to this part:

IJ.run("Analyze Particles...", "summarize slice", );
IJ.renameResults("Results");
IJ.run("Read and Write Excel", "file_mode=queue_write sheet=Mouse_"+
filename);

However, I just realized that the pop-up window that comes up"Process
Stack?" after I run "Analyze Particles" is processing all three images and
not just the one that I am currently thresholding. Is there a way to select
"no" on the "Process Stack?" window when it asks me if I want to process all
three images?
Or could I possibly select "slice 2" from the summary table to send to the
excel spreadsheet if there isn't a way to select "no"?



                       
                       





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[Cammer, Michael-2]

When thresholding and filtering composite hyperstacks, I spilt channels first and then reassemble after the processing.
Cheers-
Michael

-----Original Message-----
From: aw29 <[hidden email]>
Sent: Thursday, April 11, 2019 10:04 AM
To: [hidden email]
Subject: Selecting specific slice from the summary table

Hi!

I'm currently working on code that will allow me to threshold and analyze two channels (1 and 2) for multiple images. The first channel works perfectly, but the second one is having trouble transferring data to my excel spreadsheet because of the "Process Stack?" pop-up window. After I go through and do all of the thresholding and analysis, I get to this part:

IJ.run("Analyze Particles...", "summarize slice", ); IJ.renameResults("Results"); IJ.run("Read and Write Excel", "file_mode=queue_write sheet=Mouse_"+ filename);

However, I just realized that the pop-up window that comes up"Process Stack?" after I run "Analyze Particles" is processing all three images and not just the one that I am currently thresholding. Is there a way to select "no" on the "Process Stack?" window when it asks me if I want to process all three images?
Or could I possibly select "slice 2" from the summary table to send to the excel spreadsheet if there isn't a way to select "no"?



                       
                       





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