Re: combine data from multiple profile measurements of a time series to single data sheet

Posted by jerie on Apr 19, 2016; 7:34pm
URL: http://imagej.273.s1.nabble.com/combine-data-from-multiple-profile-measurements-of-a-time-series-to-single-data-sheet-tp5016124p5016187.html

Christopher,

you may want to look into kymographs or time-space-plots, which however are
substantially very similar to what Kota suggested.

Greetings, Jens
On 18 Apr 2016 8:34 p.m., "cpanders" <[hidden email]> wrote:

> 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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