Posted by
Herbie on
Apr 19, 2016; 7:23pm
URL: http://imagej.273.s1.nabble.com/combine-data-from-multiple-profile-measurements-of-a-time-series-to-single-data-sheet-tp5016124p5016186.html
Chris,
now you've cross-posted your question to the IJ-forum.
You can't access the values from plots after they have been saved as
images or put in a stack.
I'm still am convinced that the approach suggested by Kota works.
If you could post a partial stack (some frames) with the selection you
like to use, then one could help you much better.
"a ca. 2 mm long perpendicular line"
What does 2mm mean in pixels or what scale did you set for your images?
And to what is the line perpendicular?
Please be more specific and post an example stack.
Best
Herbie
::::::::::::::::::::::::::::::::::::::
Am 18.04.16 um 20:19 schrieb cpanders:
> I tried your suggestion but have reservations on the utility for my purpose.
> First of all , if the values represent the average over time it is not
> usable- I need data for the average profile of ca 80-100 pixels across a
> linear structure for each time point. Also, when saving image s test file
> (which is quite nice) I still am limited to a single page of data per file.
>
> There is a macro in the forum which nicely generates a profile plot for each
> frame of an image stack, but I have been unsuccessful in extracting the x-y
> data from the plot and combining it into a single data sheet/text file.
> Any suggestions? I do not ever need to see the plot, if the data can go
> directly into a file rather than being graphed I will be set.
>
>
>
>
> Here is the existing macro:
>
> // StackProfilePlot
> // This macro generates profile plots of all the images
> // in a stack and stores then in another stack.
>
> macro "Stack profile Plot" {
> ymin = 0;
> ymax = 255;
> saveSettings();
> if (nSlices==1)
> exit("Stack required");
> run("Profile Plot Options...",
> "width=400 height=200 minimum="+ymin+" maximum="+ymax+" fixed");
> setBatchMode(true);
> stack1 = getImageID;
> stack2 = 0;
> n = nSlices;
> for (i=1; i<n; i++) {
> showProgress(i, n);
> selectImage(stack1);
> setSlice(i);
> run("Plot Profile");
> run("Copy");
> w = getWidth; h = getHeight;
> close();
> if (stack2==0) {
> newImage("Plots", "8-bit", w, h, 1);
> stack2 = getImageID;
> } else {
> selectImage(stack2);
> run("Add Slice");
> }
> run("Paste");
> }
> setSlice(1);
> setBatchMode(false);
> restoreSettings();
> }
>
>
>
> --
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