In brief, my actual problem: There's some slightly noisy data, so if you see the image with your eyes, you think, hey, that's easy, the outline of this cute sea urchin is here, here and there, looking like the bisection of an apple. And then the reproducibility knocked on the door accompanied by the time you need to process quite a few images and they are friends of the common ghost called objectivity and you had to write a program.
The challenging point is the varying intensity of the image. In the middle part it gets nearly lost, but the outer part is bright and clear. By thresholding you get an image which only contains the outline, but the inside is relevant as well. So you adjust the threshold, get the inner part and lose the outline to noise... yay. And so on ;) But now it's solved!!
Where the image comes from? Actin is stained with a fluorescent dye and we want to observe the actin activity of sea urchin embryos during cell division :) But that's worth another post, sorry! ;)