Batch processing using bioformats import

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|

Batch processing using bioformats import

merchikannan
This post was updated on .
Hi ImageJ forum,

I have a trouble in automating batch processing using bioformats.
I have a bunch of FRAP image stack (in Nikon .nd2 file format).

I would like to save the first image of the FRAP image stack in a separate
folder.
However, the macro, which i'm using unable to automatically open the nd2
files.
When I run the macro, it always prompts open dialog window to select the
image stack.
the macro I'm using is below.
Any help to solve the problem is welcome!

 input = "C:/Users/GovindarajK/Desktop/Nucleus";
output = "C:/Users/GovindarajK/Desktop/Nucleus/Firstframe";

macro "files list"{
        list = getFileList(input);
        for (i=0; i<list.length; i++){
                 (list[i]); if (endsWith(list[i], ".nd2")) {
run("Bio-Formats Importer", "open= ["+ input + list[i] +"] autoscale
color_mode=Default view=Hyperstack stack_order=XYCZT");

        img_title = getTitle();
                run("Slice Keeper", "first=1 last=1 increment=2");
run("8-bit");
rename(img_title);
saveAs("Tiff", output + img_title);
close();
close();

}

        }
        }





--
Sent from: http://imagej.1557.x6.nabble.com/

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