I am quite new to the use of ImageJ and have been struggeling with a problem for quite a time now.
The first picture you see below is a histological sample of the kidney - the final aim of my project is to
find a way to take a closer look at the geometry of the brown cirlces in the tissue, the capillaries.
Therefore I try to fill the holes of these capillaries, so that the programm can later detect their circularity, perimeter, etc.
The point I’m struggeling with is the fact, that ImageJ doesn’t recognize some of the circles because of being incomplete. So on the second picture you can see the result after
- Process - Binary - Convert to Mask
- Fill Holes
On the third picture you can see another try of 1) + 2) after having edited the picture in Photoshop to desaturate the picture before, make it brighter and add more shadow to it.
As you can see, there are still cirlces that aren’t filled and other ones that are “overlapping”. I could complete the missing circles manually but despite the fact that I do have hundreds of samples this would take incredibly much time.
I would be very, very grateful for any kind of help/advice/ideas/etc.!
All the best,