Sorry if these are stupidly simple. I’m new here and will do my part in answering whatever questions I can in this forum to pay it forward. I have some imageJ commands in an .ijm macro script that I am trying to accomplish in MATLAB instead, but I’m not sure exactly how they translate. I don’t want to use MIJI or run imageJ through matlab because I want to make a standalone application.
ImageJ in bold:
selectWindow(“1”); I’m guessing this is unnecesary since I could just directly apply some function to a variable in a MATLAB script
run(“Duplicate…”, “title=white”); Also unnecessary, could just make a temporary variable that’s a copy of the image matrix
setForegroundColor(255, 255, 255); Would I just set all the elements in a matlab image array to this?
run(“Fill”, “slice”); Not sure what this does, can anyone help?
run(“Grays”); Is this a LUT? or does this just grayscale an image using the built-in function
run(“RGB Color”); No clue what this is
run(“RGB Stack”); No clue what this is
imageCalculator(“Subtract create stack”, “white”,“1”); I can understand how what it means to subtract one image from another, but what does “create stack” do?
run(“Z Project…”, “projection=[Min Intensity]”); No clue what this is
imageCalculator(“Average stack”, “img1”,“img2”); Does this average every pixel in img1 with their corresponding pixel in img2? or is it more complex?