Batch analysis

[JlvtNicolas]

Hi

I was wondering if there is a way to process batch analysis (aka: opening several stacks of images, and run the plugin to analyse all the stack one-by-one without re-lunch the analysis)?

bet regards

NJ

[HannahSHeil]

Hi
sure, the easiest way to batch process is creating a Macro to run through all files in a folder.
This is an example:

// Get path to temp directory
dir = "D:\!!!ADD PATH!!!";
print("\Clear");
savedir = "D:\!!!ADD Path!!!";

list = getFileList(dir);
setBatchMode(true);
for (i = 0; i < lengthOf(list); i++) {
// for (i = 0; i < 1; i++) {
if (endsWith(list[i], ".nd2")){
print("---------------------");
print(list[i]);
print("---------------------");
run("Bio-Formats Windowless Importer", "open=["+dir+"\"+list[i]+"]");
run("eSRRF - Analysis", "magnification=5 radius=1.50 sensitivity=3 #=100 vibration avg wide-field #_0=25 axial=400");

	selectWindow(list[i]+" - eSRRF (AVG)");
	saveAs("Tiff", savedir+"//"+list[i]+" - eSRRF (AVG)"+".tif");
	//selectWindow(list[i]+" - eSRRF (STD)");
	//saveAs("Tiff", savedir+"//"+list[i]+" - eSRRF (STD)"+".tif");
	selectWindow(list[i]+" - interpolated image");
	saveAs("Tiff", savedir+"//"+list[i]+" - interpolated image"+".tif");
	run("Close All");
}

}

setBatchMode(false);
print("-----------------");
print("All done.");

Let me know if you need more support.
Best, Hannah