Macro to make Z-projections from .lif stacks

[Luis Boero]

Hi! I´ve been trying to develop a macro to get z projections from the stacks I take in the microscope.

run("Bio-Formats Macro Extensions");
inputFolder=getDirectory("");
images=getFileList(inputFolder);
NewDir=inputFolder+"Procesadas";
//File.makeDirectory(NewDir); // creo la carpeta

for (i=0; i<images.length; i++) {
        path=inputFolder+images[i];
        filename=images[i];
        Ext.setId(path);
        Ext.getSeriesCount(seriesCount);
       
        for (j=1; j<=seriesCount; j++) {
                       
                run("Bio-Formats", "open=path autoscale color_mode=Default view=Hyperstack split_channels stack_order=XYCZT,j);
               
                list = getList("image.titles");
  if (list.length==0)
             print("No image windows are open");
  else {
             //print("Image windows:");
             for (k=0; k<=list.length; k++) {
            print("   "+list[k]);
            selectWindow();
            run("Z Project...", "projection=[Max Intensity]");
            close(title);
  }
  }
}

When I run the macro, I only get the Max Projection from the channel that corresponds to k=1, but the other one remains as a substack. What can I do?

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[Luis Boero]

Sorry, I make a mistake at the latest at the line 30

close(title);

should say

close();

However, the problem remains.

Thanks in advance.

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[Olivier Burri]

Hi Luis,

Might it be that your selectWindow() is not taking an argument, right at the end of your code?

To get to working, try changing it to
selectImage(list[k]);
and then running your Z-Project

If you run the close(); right after your projection, you will close it before finishing.

Either save your image before or run
selectImage(list[k]);
again before the close command.

Best

Oli

> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Luis
> Boero
> Sent: mercredi, 6 juillet 2016 21:48
> To: [hidden email]
> Subject: Macro to make Z-projections from .lif stacks
>
> Hi! I´ve been trying to develop a macro to get z projections from the stacks I
> take in the microscope.
>
> run("Bio-Formats Macro Extensions");
> inputFolder=getDirectory("");
> images=getFileList(inputFolder);
> NewDir=inputFolder+"Procesadas";
> //File.makeDirectory(NewDir); // creo la carpeta
>
> for (i=0; i<images.length; i++) {
> path=inputFolder+images[i];
> filename=images[i];
> Ext.setId(path);
> Ext.getSeriesCount(seriesCount);
>
> for (j=1; j<=seriesCount; j++) {
>
> run("Bio-Formats", "open=path autoscale color_mode=Default
> view=Hyperstack split_channels stack_order=XYCZT,j);
>
>                 list = getList("image.titles");
>   if (list.length==0)
>              print("No image windows are open");
>   else {
>              //print("Image windows:");
>              for (k=0; k<=list.length; k++) {
>             print("   "+list[k]);
>             selectWindow();
>             run("Z Project...", "projection=[Max Intensity]");
>             close(title);
>   }
>   }
> }
>
> When I run the macro, I only get the Max Projection from the channel that
> corresponds to k=1, but the other one remains as a substack. What can I do?
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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