//choose a macro mode and a directory
#@ String (label=" ", value="Rectangle Crop
Batch processing", visibility=MESSAGE, persist=false) heading
#@ File(label="Select a directory:", style="directory") dir
#@ File (label="Select an image", style="file") file
#@ String (label=" ", value="![](\"https://live.staticflickr.com/65535/48557333566_d2a51be746_o.png\")
", visibility=MESSAGE, persist=false) logo
#@ String (label=" ", value="Neuromolecular Biology Lab
ERI BIOTECMED - Universitat de València (Spain)", visibility=MESSAGE, persist=false) message
//create the selection
open(file);
setTool("rectangle");
waitForUser("Make a rectangular selection");
selection=selectionType(); // 0 = rectangle
while (selection != 0) {
setTool("rectangle");
run("Select None");
waitForUser("Make a rectangular selection");
selection=selectionType();
}
roiManager("add");
run("Close All");
//crop images
setBatchMode(true);
print("Start batch process");
list=getFileList(dir);
dirName=File.getName(dir);
dirParent=File.getParent(dir);
outputDir=dirParent+File.separator+dirName+"_Crop";
File.makeDirectory(outputDir);
for (i=0; i