Dear ImageJ experts,
I want a semi-automatic way to measure the area of neuron cell bodies.
I would like ImageJ to:
open an image (my images are Zeiss lsm files - I have the macro that opens those installed),
split the channels,
close the channels I don't need,
threshold the channel I am interested in,
fill in holes,
apply watershed to separate the cell body from the neuronal processes,
display the image (or rather, the channel i am interested in) and wait for me to click on what I deem to be neuronal cell bodies and measure those,
close the image and open the next one, or at least take me to the directory where I got the previous picture.
I have tried various things, but tend to run into trouble with the automatic opening and closing of the images, with displaying them for me to work on, or with waiting for me to do stuff with the image. Below is the code I have come up with.
I would be immensely grateful for help and suggestions!
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dir = getDirectory("Choose a Directory "); list = getFileList(dir); setBatchMode(true); for (i=0; i<list.length; i++) { showProgress(i, list.length); open(dir+list[i]);
title = getTitle();
run("Split Channels");
selectWindow("C1-"+title);
close();
selectWindow("C2-"+title);
close();
selectWindow("C3-"+title);
close();
selectWindow("C4-"+title);
setAutoThreshold("Default dark");
run("Convert to Mask");
run("Fill Holes");
run("Watershed");
//setTool("wand");
run("Set Measurements...", "area mean perimeter display add redirect=None decimal=3");
waitForUser(“Click on cell bodies, measure and then click ok”)
close; }
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