Loop for time points

[LP]

Dear ImageJ community,

I wrote the following macro that basically uses the first channel to create a mask on the second channel and then clears everything that's out of the mask. It works fine on my Z-stacks.

However I have multiple time points and I don't know how to make the following macro go to the next time point once it did the first one.

So basically I'd like to add before my line 5 the equivalent of "for (s = 1; s < nSlices(); s++){ " but for time points.
_________________________
name = File.nameWithoutExtension();
setBatchMode(false);

                function (Splitchannel){
                        run("Split Channels");

                for (s = 1; s < nSlices(); s++){
               
                        selectWindow("C1-"+name + ".tif");
                        setAutoThreshold("Default dark");
                        run("Create Mask");
                        setOption("BlackBackground", false);
                        run("Dilate");
                        run("Dilate");
                        run("Dilate");
                        run("Dilate");
                        run("Dilate");
                        run("Dilate");
                        run("Dilate");
                        run("Dilate");
                        run("Create Selection");
                        roiManager("Add");

                        selectWindow("C2-"+name + ".tif");
                        roiManager("Select", 0);
                        setBackgroundColor(0, 0, 0);
                        run("Clear Outside", "slice");
                        roiManager("Deselect");
                        roiManager("Delete");
                        selectWindow("mask");
                        close();

                        selectWindow("C2-"+name + ".tif");
                        run("Next Slice [>]");
                        selectWindow("C1-"+name + ".tif");
                        run("Next Slice [>]");
                }

run("Merge Channels...", "c1=[C1-"+name + ".tif] c2=[C2-"+name + ".tif] create");
Stack.setDisplayMode("color");
run("Save");
close();
__________________________

Any suggestion and help will be very appreciated.

Thank you very much for your help in advance,
LP

[Rasband, Wayne (NIH/NIMH) [E]]

> On Dec 10, 2016, at 5:39 PM, LP <[hidden email]> wrote:
>
> Dear ImageJ community,
>
> I wrote the following macro that basically uses the first channel to create
> a mask on the second channel and then clears everything that's out of the
> mask. It works fine on my Z-stacks.
>
> However I have multiple time points and I don't know how to make the
> following macro go to the next time point once it did the first one.
>
> So basically I'd like to add before my line 5 the equivalent of "for (s = 1;
> s < nSlices(); s++){ " but for time points.

Use the Stack.getDimensions(w,h,c,z,t) function to get the number of time points and Stack.setPosition(c,z,t) to set the time point in a loop. The following example macro opens the Mitosis sample stack and inverts the second (green) channel of the third slice of each time point.

  run("Mitosis (26MB, 5D stack)");
  Stack.getDimensions(width,height,channels,slices,frames);
  for (t=1; t<=frames; t++) {
     Stack.setPosition(2, 3, t);
     run("Invert", "slice");
  }

-wayne

> _________________________
> name = File.nameWithoutExtension();
> setBatchMode(false);
>
> function (Splitchannel){
> run("Split Channels");
>
> for (s = 1; s < nSlices(); s++){
>
> selectWindow("C1-"+name + ".tif");
> setAutoThreshold("Default dark");
> run("Create Mask");
> setOption("BlackBackground", false);
> run("Dilate");
> run("Dilate");
> run("Dilate");
> run("Dilate");
> run("Dilate");
> run("Dilate");
> run("Dilate");
> run("Dilate");
> run("Create Selection");
> roiManager("Add");
>
> selectWindow("C2-"+name + ".tif");
> roiManager("Select", 0);
> setBackgroundColor(0, 0, 0);
> run("Clear Outside", "slice");
> roiManager("Deselect");
> roiManager("Delete");
> selectWindow("mask");
> close();
>
> selectWindow("C2-"+name + ".tif");
> run("Next Slice [>]");
> selectWindow("C1-"+name + ".tif");
> run("Next Slice [>]");
> }
>
> run("Merge Channels...", "c1=[C1-"+name + ".tif] c2=[C2-"+name + ".tif]
> create");
> Stack.setDisplayMode("color");
> run("Save");
> close();
> __________________________
>
> Any suggestion and help will be very appreciated.
>
> Thank you very much for your help in advance,
> LP
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Loop-for-time-points-tp5017753.html
> Sent from the ImageJ mailing list archive at Nabble.com.

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html