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";
<create the table here>
processFolder(input, output);
function processFolder(input, output) {
list = getFileList(input);
for (i = 0; i < list.length; i++) {
if(File.isDirectory(input+list[i]))
processFolder(input + list[i]);
if(endsWith(list[i], suffix))
processFile(input, output, list[i]);
}
<save the table into the output folder here>
}
function processFile(input, output, file) {
open(input + file);
run("Find Maxima...", "noise=80 output=[Point Selection] exclude");
<use the command waitForUser to let the user correct the point selection before the execution continues>
getSelectionCoordinates(xpoints, ypoints);
row = <get the size of the table Counts>
count = <get the length of the array xpoints>
<add the name of the image to the table in the column Image and the current row>
<add the number of objects to the table in the column Count and the current row>
close();
}