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rename to match imagej naming convention

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Adien Akhmad 2026-02-21 11:04:26 +07:00
parent 9da624879a
commit d865a4198c
1 changed files with 0 additions and 0 deletions
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82
particle-beads.ijm
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@ -1,82 +0,0 @@
inputDir = getDirectory("Choose Input Directory");
outputDir = inputDir + "particle_analyze" + File.separator;
if (!File.exists(outputDir)) {
File.makeDirectory(outputDir);
}
// config - roi styling
roiColor = "yellow";
roiThickness = 3;
fillColor = "none";
// prepare the environment (Clear old results/summaries)
run("Clear Results");
if (isOpen("Summary")) {
selectWindow("Summary");
run("Close");
}
list = getFileList(inputDir);
setBatchMode(true);
for (i = 0; i < list.length; i++) {
if (endsWith(toLowerCase(list[i]), ".png")) {
processFile(inputDir, outputDir, list[i]);
}
}
setBatchMode(false);
if (isOpen("Summary")) {
selectWindow("Summary");
saveAs("Results", outputDir + "Summary_Report.csv");
}
if (isOpen("Results")) {
selectWindow("Results");
run("Close");
}
print("Done! Files and summary saved to: " + outputDir);
function processFile(input, output, filename) {
// Clear ROI Manager for each new image
if (roiManager("count") > 0) {
roiManager("deselect");
roiManager("delete");
}
open(input + filename);
// create a filename for the output
basename = File.nameWithoutExtension;
newName = basename + ".png";
run("Set Scale...", "distance=2691 known=1000 unit=micron global");
run("Specify...", "width=2691 height=2691 x=476 y=476 constrain");
run("Crop");
currentImage = getTitle();
// prepare binary image for analyzer
run("Duplicate...", " ");
setThreshold(0, 85, "raw");
setOption("BlackBackground", true);
run("Convert to Mask");
run("Fill Holes");
run("Watershed");
run("Analyze Particles...", "size=78.5-120 circularity=0.75-1.00 display exclude clear summarize add");
close();
// select the cropped image and save it with the ROIs
selectImage(currentImage);
if (roiManager("count") > 0) {
roiManager("deselect");
roiManager("Set Color", roiColor);
roiManager("Set Line Width", roiThickness);
roiManager("Show All without labels");
run("Flatten");
saveAs("PNG", output + newName);
}
run("Close All");
}