I am new to ImageJ and I am stuck with my analysis now.
I have gray scale images and managed to do the analysis on each single image by drawing a straight line for my ROI and retrieving the plot profile (of gray scae values) and its maxima/minima by running the macro “Extrema of current line profile” (found here: https://imagej.nih.gov/ij/macros/examples/FindMaxima1D.txt).
However, I would like to run the macro for many (>80) images and this is where I am stucked now.
I made different attempts so far:
using macro “Stack profile Plot” (https://imagej.nih.gov/ij/macros/StackProfilePlot.txt) -> Plots are created as images thus not accessible for i.e. “Find peaks” (BAR), as plots are required. -> cannot proceed to find local maxima/minima.
Align all images to a stack -> straight line for ROI was drawn on the first slide -> “Stack to Images” ignores the line selection. I would have to draw the ROI (straight line) for each image again.
Drawing a line from “Overlay Brush” on a stack of images (and then use stack to images) will eventually give me every image with the line selection, however the line was not recognized as line selection by the macro “Extrema of current line profile”.
I am aware of the option of Process -> Batch for Batch Processing. But Ifor that, I need each single image with line selection.
How can I solve this problem? I think if I manage to use the “stack to Image” option to save each single image with the line selection, I can proceed with the batch function?
Your help is much appreciated! Thank you!