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Dear ImageJ Experts,
I wrote a little macro for image preprocessing:
1. Open a couple of images.
2. Execute the menu item 'Image - Stack - Images to Stack'.
3. Extract the background by executing 'Image - Stack - ZProjection' and selecting 'Min Intensity' in the user dialog.
4. Substract the background using the command 'Process - Image Calculator'. Use 'Stack' as the source, 'Substract' as the operation and 'MIN_Stack' as the substrahend.
5. Dissolve your stack with 'Image - Stack - Stack to Images'.
6. Save the images.
Here is my code:
macro "Remove static background and save Action Tool - C000T2f20S" {
run("Close All"); //No image must be opened !
showMessage("Choose source directory for static background reduction")
dir1 = getDirectory("Choose source directory for static background reduction");
run("Image Sequence...", "open=[dir1] sort");
rename("Stack");
run("Z Project...", "start=1 stop=100 projection=[Min Intensity]"); //Generate a new image with the static background
idz = getImageID();
imageCalculator("Subtract stack", "Stack","MIN_Stack"); // Remove static background from all images in the stack
selectImage(idz); // close image of static background
close();
//run("Enhance Contrast", "saturated=0.05 normalize_all"); // Enhance contrast of all images from stack
chooseBatch=1;
run("Stack to Images"); //disassemble the stack to get single images with reduced static background
while(chooseBatch == 1) {
// get image IDs of all open images
ids=newArray(nImages); //new Array, containing the ids of all opened images
for (i=0;i<nImages;i++) {
selectImage(i+1);
rename(i+1);
ids[i]=getImageID;
}
// process all open images
for (i=0;i<ids.length;i++) {
showProgress(i+1, ids.length);
// If all opened images from the input folder have been processed, the batch process is finished.
if (i+1==ids.length) {chooseBatch = 0; }
///////////////////////////////////
//What will be done with each image
///////////////////////////////////
setBatchMode(true);
selectImage(ids[i]);
if (i<10)
j="0"+i;
else j=i;
saveAs("Tiff", dir2+j+"_processed");
close();
setBatchMode(false);
///////////////////////////////////
//What will be done with each image
///////////////////////////////////
}
}
staticBackgroundRemoved = true;
print("Static background has been removed! Now you can run the batch process!");
}
How can I modify this code, to load a set of folders and treat the content of this folder the way my macro doe ?
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