Making standard measurement of 100 samey tiny pieces at one shot


#1

Hi everyone!
I would be extremely thankful if one could suggest the way to solve my problem.
I’ve got dozens photos of elements of urchins, each photo contains approximately 100 elements, which never cross with each other. All the elements are the same actually, they all are rectangular like at the photo below :

I am to measure the smallest length of all the pieces at each photo.
So I wonder if there any way to carry out an automatic measurement of all the elements at each photo. For example, I could make the first measurement or select the element somehow to help machine to understand what exactly do I want from it. Any ideas?)

Thanks in advance!


#2

ok @Mitya_Vasyukov

So I am no expert here… but here is something you can at least start with and see if it helps… it’s not perfect (as there is overlap between some objects, making them more difficult to individualize - but you can always remove those objects as outliers based on area or so…).

Here is a little macro I came up with to segment/measure your objects:

setAutoThreshold("Otsu dark");
//run("Threshold...");
run("Create Mask");
run("Fill Holes");
run("Analyze Particles...", "display exclude add");

If you look at the list of measurements calculated in Set Measurements. The major axis of the ellipse for Fit Ellipse might do the trick.

But perhaps others have more refined methods… I’d be happy to learn them myself.

eta :slight_smile:


#3

Another noob’s step-by-step advice:

  1. set scale (otherwise, all measurements will be in pixels; I used the length of object #11 as 1 mm)
  2. convert to 8-bit
  3. adjust threshold
  4. Important: use the line drawing tool (black single pixel-wide line) to separate the overlapping particles by one pixel-wide channels
  5. use Particle Analysis to get the attached result.

    The distribution chart uses mini-Feret (width) of the particles, but of course you can pick the length or any other column from the Results table for this chart.

I bet true experts can improve on this simplistic process, but it works for me.