I have been using CellProfiler for a few days now, and I am very impressed with the program so far. I counted the cells using the following modules: LoadImage > ColorToGray > IdentifyPrimaryObjects (a picture of the settings is attached)
However, there are some minor issues in counting the cells, and I was hoping someone from this forum could help me with them.
The first issue is regarding the unclear sections of my images (check the attached example). I would like to exclude them from there so the program does not attempt analyzing them. These sections include the background noise and the areas that contain cells with low color intensity. Is there any way to exclude regions with low intensity from the image? Basically what I would like to do is to exclude the noisy pixels of the image so CellProfiler distinguishes the cells easier.
The second issue is that the program sometimes counts a small portion of the same cell as another cell (just like the example in image 2). Also, sometimes the somas of the neurons are clumped together and are counted as one. Is there any way to make the program count cells that are bigger than a certain surface area as two cells? And is the problem in image 2 solvable?
The original and the analyzed images are also attached to this post.