![]() ![]() The currently shown slice can also be duplicated with target=round(nSlices*0. Does anybody know why this doesn’t appear to work?įinally, do you actually need to make a substack? Rather than creating substacks, you could just select the slice of interest (setSlice(), Built-in Macro Functions) and do your analysis/measurements on that slice. If the thresholded image is satisfactory, the user can click the Apply button to apply the thresholding. The thresholded image can be previewed in the window. However, this doesn’t appear to work for ‘Make Substack’. Once the thresholding method is selected, the user can adjust the threshold level using the slider or by entering a value in the box. Run("Make Substack.", " slices="+targetSlice) Īccording to the documention, it should also work to simply precede the variable name that you want to pass as a parameter with & (see ). So, if targetSlice holds the position of your slice, you could use : //round() rounds the number to the nearest integer, so round(nSlices*0.5) sets the middle slice of a stack) If you want to pass a variable as an argument to a function, you can use string concatenation: If anyone has any suggestions about how I can alter the above code so it works or go about the task in a different way I would really appreciate the help The code run(“Make Substack…”, “slices=_” will not work with a fraction. Setting a threshold can be a very subjective process because the user may impose user’s own criteria to accept the desired pore diameter. In the Threshold window, pixels that are within the red box are being selected. Obtained pore information from the graphical process using the ImageJ is very subjective and uncertain. (Although it has color, this is not a RGB image). Depending on the stack when dividing it by 2 it might not be a whole number. ASHOK (ashok dewangan) April 6, 2016, 1:04pm 1.This code run(“Make Substack…”, " slices= ") will not accept my variable name as the input after “slices= _”.run(“Make Substack…”, “slices= “centerSlice””) and this would pick out the slice in the middle of the stack for me to analyse on its own. ![]() centerSlice= nSlices/2 and bottomSlice= nSlices - 10Į.g. This submenu contains commands that adjust brightness/contrast, window/level, color balance, threshold levels and image/canvas size. I was thinking I could make a variables e.g. The command nSlices tells you how you how many slices there are in your stack. run(“Make Substack…”, “slices=10”) would be the slice I analyse as top of my sample. My way of going about this was to create a substack of just one slice from each of these positions using the code run(“Make Substack…”, “slices=_”) soĮ.g. 10 slices away from the end of the stack). Thresholding is a technique for dividing an image into two (or more) classes of pixels, which are typically called foreground and background. 10 slices in, as sample is inverted) then the center slice and then close to the end (e.g. I was thinking to do this by selecting a slice in my z-stack that was close to the start of stack as the top (e.g. I’m looking write a macro that will analyse cells at the ‘top’, center and ‘bottom’ of my sample. ![]()
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