"Analyze skeleton" & Analyze particles order of object proceccisng

Hey there!

I am writing a fiji macro to analyze cell morphology. I was asking for help before and @schmiedc helped me with great tips. Thank you so far!

As i try to make my script less complicated at the moment, i was wondering whether somebody knows, in which order the “Analyze Particles” and “Analyze Skeleton” processes analyze the objects in a picture.

background: I want to have both analyzing processes one after another on a huge Image with multiple objects and hope to be able to put the results-tables next to each other or even put them together in imagej already (as schmiedc suggested). This is why i have to be sure, that both prompts analyze the objects in the same order.

Thank you for your time and efforts,

best wishes, Peter

Hi @prein,

just guessing, this is the thread where you discussed with @schmiedc, right?

Regarding your question: If the analysis of particles and skeleton are independent from each other (are they?). The order should not matter. To be absolutely sure, you can organise your code with custom functions like this:

filename = "example.tif";

myParticleAnalysis(filename);

mySkeletonAnalysis(filename);



function myParticleAnalysis(filename) {
    open(filename);
    // here comes the analysis workflow using particle analyser
    close("*"); // close all images
}

function mySkeletonAnalysis(filename) {
    open(filename);
    // here comes the analysis workflow using skeletonization
    close("*"); // close all images
}

You could then also comment out the second or third line to see if the result of the other analysis stays the same.

Let us know if this helps or if you need further support.

Cheers,
Robert

1 Like

Hey Robert,

you’re absolutely right :wink:
I would like to bring both results together and put them in correlation, this is why i want both analyses to process the objects in the same order, as i could match the results tables afterwards then.

For organization of the macro, you’re tip is great, i will think about that! Thank you!

Cheers, Peter