Aim:
The macro will work on all tif images in a folder and all subfolders.
It will count the objects in an image by detecting the maxima.
Use the waitForUser command to pause the execution and let the user correct the count for each image!
Use the commands
Table.create( )Table.size( )Table.set( )Table.save( )to create and save a table Counts and to add a row containig the name of the image and the number of objects for each image.
Run the macro on the folder images/15!
input = getDirectory("Input directory");
output = getDirectory("Output directory");
suffix = ".tif";
Table.create("Counts");
processFolder(input, output);
function processFolder(input, output) {
list = getFileList(input);
for (i = 0; i < list.length; i++) {
if(File.isDirectory(list[i]))Table
processFolder(input + list[i], output);
if(endsWith(list[i], suffix))
processFile(input, output, list[i]);
}
Table.save(output + "Counts.xls", "Counts");
}
function processFile(input, output, file) {
open(input + file);
run("Find Maxima...", "noise=80 output=[Point Selection] exclude");
waitForUser("Correct and press ok!");
getSelectionCoordinates(xpoints, ypoints);
row = Table.size("Counts");
count = xpoints.length;
Table.set("Image", row, file, "Counts");
Table.set("count", row, count, "Counts");
close();
}
| Image | count |
|---|---|
| A4 dapi 1.tif | 10 |
| nuclei.tif | 40 |
| two-nuclei.tif | 2 |