I got some help to define the images to be pre-processed:
Now I would like to run a plugin to identify the objects that overlap in several channels. This script opens them but I can’t get how to define them in the plugin and save the pooled results later. I would really appreciate some help.
May be this can help.
// Get the folders first
#@File directory (style=“directory”);
subfolders = getFileList( directory )
// Go through each folder
for ( i=0; i<subfolders.length; i++ ) {
// Check that it is a folder
if ( endsWith( subfolders[i], “/” ) ) {
//Open sub images
image_name = substring( subfolders[i] , 0, lengthOf( subfolders[i] ) -1 );
// Open object images here
open(directory + "/" + subfolders[i] + image_name + "CH2_objects.tif");
open(directory + "/" + subfolders[i] + image_name + "CH4_objects.tif");
run("Binary Feature Extractor", "objects= directory + "/" + subfolders[i] + image_name + "Iba1_objects.tif" selector=directory + "/" + subfolders[i] + image_name + "DAPI_objects.tif"_overlap=30 count"); //extract double positive objects with overlap 30%
run("Binary Feature Extractor", "objects= Here I want to add the results of the first binary feature (file starts with extracted)" selector=directory + "/" + subfolders[i] + image_name + "CH3_objects.tif"_overlap=20 count"); //extract Triple positive objects with overlap 20%
Then I want to save the pooled results of the count including the image label to be able to identify it.
}
}
