First and foremost, I am very new to microscopy, and even more so with CellProfiler, so I apologize if this question is basic. I am working with someone in my lab on measuring the area of satellite cells, and I’m running into some problems with the analysis picking up too much of the background. I have gone through the CellProfiler tutorials, and have done some other ones, but I have yet to figure out how to get my pipeline to quit picking up so much noise.
The images I have taken were done using brightfield microscopy, and I think therein lies the problem. The background of the image and the cells are similar on the grayscale, and thresholding is almost impossible. My question then is, is there a module that will allow me to better differentiate between background and foreground? Or would it be better if we just retake our images with fluorescence so we can separate the two?
As this is my first post, I am unable to attach any files, but they will follow in a subsequent comment.