Measuring length/ width of rod shaped (irregular) fungal spores


I’m trying to measure the length and width of a large number of fungal spores.

This is what the original image looks like. I have been able to make it 8-bit, and have tried to change the threshold values to make the spore outline clear. However, I think shape of the spores may be problematic. It seems like the analyse particle option may not work here. Is a macro of some sort required?

I’m very new to this program and not terribly tech savvy, so any help is hugely appreciated,


Since your spores look like bacteria, I would give a shot at Oufti before ImageJ.
Tell us what you think if you try it.

You can extract your shapes with the find edges action and then apply filters to smooth the inner structure of the spores (try different filters and settings!), something like:

run("Find Edges");
run("Median...", "radius=20");
setOption("BlackBackground", false);
run("Make Binary");
run("Fill Holes");

which results in:

Then you can analyze the particles and exclude the smaller “dirt” (here I used a decreased image so you have to adjust it) and edge particles if you like:

run("Set Measurements...", "area mean min centroid perimeter bounding shape feret's stack limit display redirect=None decimal=5");
run("Analyze Particles...", "size=100-Infinity display exclude add");

Here one result:

Here you can find the description of the the options for the measurements:

There are also several plugin available to measure different shape parameters, see:

And here some valuable resources from the forum:

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