Running/Editing Macros on Windows

imagej

#1

Hi,

I have a macro for counting the DAPI stained nuclei and GFP fluorescent cells. However, if I change the threshold and then try and save the macro with new threshold it doesn’t let me do it. It changes back to the initial threshold when I go on to the next image. This problem doesn’t happen with a colleague who uses Mac.
Can anyone please help me to sort this out?

Thanks


#2

Dear @Spandan_Kalra,

Please describe what you mean by “It doesn’t let me do it”. Perhaps your macro in in a write-protected folder?

Best case, please share the macro so that the helpful gurus here can help you troubleshoot the issue.

Best


#3

You can’t edit a macro while its running to change how it functions. The changes are made outside of the currently running script, you would have to terminate the macro and restart to apply the changes.

If you want to adjust the threshold on the fly during the macro, I would suggest allowing the user to alter it by either using:

run("Threshold...");
waitForUser("Adjust threshold");

OR

lower = getNumber("Lower threshold", 0);
upper = getNumber("Upper threshold", 255);
setThreshold(lower, upper);

If you are changing the threshold for each image, be careful with biasing your results, you should ideally find a threshold that suits all of your images or a set of processing steps that will give you your desired results and doesn’t change each time. Your imaging should also be done with consistent acquisition settings, so that you can make comparisons between images. Just thought I’d mention this, depends on what you’re using your results for.

Best,

Rob