Re: combine data from multiple profile measurements of a time series to single data sheet

Posted by Herbie on Apr 22, 2016; 6:54pm
URL: http://imagej.273.s1.nabble.com/combine-data-from-multiple-profile-measurements-of-a-time-series-to-single-data-sheet-tp5016124p5016220.html

Good day Christopher,

nice to see that you found a way of performing the desired task.

In addition I should like to propose an example macro based on Kota's approach. The essential part of it is quite concise.

-- You need an open internet connection to run the macro. --

// example macro (watch for mailer line breaks!)
width = 15; // integration width perpendicular to the line selection

// the following is for the generation of an test image only
run( "Confocal Series (2.2MB)" );
setBatchMode( true );
name = "TestStack";
Stack.setDisplayMode( "grayscale" );
run("Reduce Dimensionality...", "slices");
run( "Set Scale...", "distance=0" );
setLineWidth( 0 );

// example line selection for the profile
makeLine( 66, 328, 218, 176 );

// here comes the beef ---------------------------------------------
run( "Reslice [/]...", "output=1.000 slice_count="+width+" rotate");
run( "32-bit" );
run( "Z Project...", "projection=[Average Intensity]" );
rename( "ProfileValues_of_" + name );
saveAs( "Text Image" );
setBatchMode( "exit and display" );
// end of beef tail ------------------------------------------------

The text file that you are going to save contains the profile values in columns. Each column contains the profile values from one frame.

Please note that the integration starts from the selection line downwards. In the example case 15 pixels wide.

Best

Herbie