quantification of cell spreading

timelapse-stacks-v105.txt

 

//Macro for ImageJ by

//Michael Cammer cammer@aecom.yu.edu for AIF www.aecom.yu.edu/aif/

//Data presented or published using this/these macro(s)/function(s) or modification(s) thereof

//must acknowledge the "Analytical Imaging Facility at the Albert Einstein College of Medicine"

//and ImageJ as explained at rsb.info.nih.gov/ij/docs/faqs.html

 

// Michael Cammer 20030118

// macros for cleaning up time series data

//---------------------------------------------

// User selects a ROI in the background of a stack.

// This ROI is measured in each slice and the mean value of each slice is subtracted

// from the correct slice. This corrects for variation in background value over time.

 

function checkCurrentVersion(){

requires('1.38d');

}

 

 

macro 'Subtract background based on ROI'{

checkCurrentVersion();

run("Set Measurements...", " mean redirect=None decimal=0");

run("Plot Z-axis Profile"); run("Close");

for (i=1; i<=nSlices; i++){

bgmean=getResult("Mean",(i-1));

run("Set Slice...", "slice="+i);

run("Select All");

run("Subtract...", "slice value="+bgmean);

}

 

 

 

//-----------------------------------------------

macro 'Multiply to fix bleaching based on ROI'{

checkCurrentVersion();

original = getImageID();

run("Set Measurements...", " mean redirect=None decimal=0");

run("Plot Z-axis Profile"); run("Close");

standard = getResult("Mean",(0));

selectImage(original);

for (i=1; i<=nSlices; i++){

bgmean = standard / getResult("Mean",(i-1));

run("Set Slice...", "slice="+i);

run("Select All");

run("Multiply...", "slice value="+bgmean);

}

 

 

//-----------------------------------------------

macro "paste with blend adjacent slices"{

checkCurrentVersion();

original = getImageID();

selectImage(original);

for (i=2;i<=nSlices;i++) {

run("Set Slice...", "slice="+i); run("Select All"); run("Copy");

run("Set Slice...", "slice="+(i-1)); setPasteMode("Average"); run("Paste");

}

selectImage(original);

run("Set Slice...", "slice="+nSlices); run("Delete Slice");

run("Set Slice...", "slice="+1); run("Delete Slice");

run("Brightness/Contrast...");

}

 

//------------------------------------------

macro "paste with subtract adjacent slices"{

checkCurrentVersion();

original = getImageID();

selectImage(original);

for (i=2;i<=nSlices;i++) {

run("Set Slice...", "slice="+i); run("Select All"); run("Copy");

run("Set Slice...", "slice="+(i-1)); setPasteMode("Subtract"); run("Paste");

}

selectImage(original);

run("Set Slice...", "slice="+nSlices); run("Delete Slice");

run("Set Slice...", "slice="+1); run("Delete Slice");

run("Brightness/Contrast...");

}

//--------------------------------

 

macro "make test image"{

checkCurrentVersion();

x=0; y=0;

for (i=1;i<=nSlices;i++) {

run("Set Slice...", "slice="+i);

setPixel(x, y, 255); setPixel(round(x*1.25), y, 255);

setPixel(100+(2*random()), 80+(2*random()), 255);

x=x+1; y=y+1;

}

}

 

 

//------------------------------------------------------------------

macro 'Projections of variable width'{

checkCurrentVersion();

original = getImageID();

end = nSlices();

zdepth = 4;

projtype = "'Max Intensity'" ; // or 'Average Intensity' or some other type

for (i=1;i<(end-zdepth);i++){

stop = i + zdepth;

run("Z Project...", "start="+i+" stop="+stop+" projection="+projtype);

run("Select All");

run("Copy");

run("Close");

selectImage(original);

run("Set Slice...", "slice="+i);

run("Paste");

}

 

}

//-------------------------------------------------------------------

macro "Subtract adjacent slices in a stack SLOW"{

checkCurrentVersion();

original = getImageID();

height = getHeight(); width = getWidth(); bits = bitDepth();

run("New...", "name=early type="+bits+"-bit fill=White width="+width+" height="+height+" slices=1");

early = getImageID();

run("New...", "name=late type="+bits+"-bit fill=White width="+width+" height="+height+" slices=1");

late = getImageID();

selectImage(original);

run("Set Slice...", "slice=1"); run("Select All"); run("Copy");

selectImage(late);

run("Paste");

selectImage(original);

for (i=2;i<=nSlices;i++) {

tempvalue = early; early = late; late = tempvalue;

run("Set Slice...", "slice="+i); run("Select All"); run("Copy");

selectImage(early);

run("Paste");

run("Image Calculator...", "image1=late operation=Subtract image2=early create ");

run("Select All"); run("Copy"); run("Close");

selectImage(original);

run("Set Slice...", "slice="+(i-1)); run("Paste");

}

selectImage(early); run("Close");

selectImage(late); run("Close");

selectImage(original); run("Set Slice...", "slice="+nSlices); run("Delete Slice");

run("Set Slice...", "slice="+1); run("Delete Slice");

run("Brightness/Contrast...");

}

//------------------------------------------

 

Done