Collecting the results of a batch analysis into a single file

Usage & Issues
#1

Hi,
I recorded the following macro to measure the volume of gfp labelled glomeruli.

run("3D Objects Counter", "threshold=30 slice=7 min.=200 max.=117124 objects surfaces centroids centres_of_masses statistics summary");

It works when I run it as a batch command but with one problem - it creates a separate results window for each image, I would like it to tabulate the results in one table. Is there a way of doing this?

Thank you

#2

Most likely. However, I am not familiar with 3d objects Counter. Could you provide a screenshot of what the multiple results tables look like?

#3

Thanks for your reply,
This is what the text output looks like:

13%20PM
13%20PM2624×2154 115 KB

#4

Hi,

This is what I get:

image1.png

Thanks

Simon

#5

I was going to post the following. Based on what I have read about creating a new table, it should work. However, I have not been able to get it to work because Fiji/ImageJ seems to not recognize the new table as a table; even when using the command run("New... ", "title=["+combined_results+"] type=Table").

Okay, I am assuming that the title of those windows are just the image names preceded by “Statistics for”. You could try having the macro code be something like this.

combined_results = "your title here";
image_title = getTitle();
single_results = "Statistics for "+image_title;
print_string = image_title;
run(“3D Objects Counter”, “threshold=30 slice=7 min.=200 max.=117124 objects surfaces centroids centres_of_masses statistics summary”);
selectWindow(combined_results);
num_results = getValue("results.count");
IJ.renameResults("Temporary Results Rename");
IJ.renameResults(single_results, "Results");
for (i = 0; i < column_titles.length; i++) {
    print_string = print_string+"\t"+getResultString(column_titles[i], 0);
}
print("["+combined_results+"]", print_string);
close("Results");
IJ.renameResults("Temporary Results Rename", "Results");

Before you run it, you would just need to open a new table window and name it whatever name you give in the script.