Does brightness/contrast change the of color image change the result of corresponding binary image?

I have a set of color images and want to convert them to binary images for further analysis. During the process of conversion to binary, some of the images need a very low threshold to avoid whole black image but some of them does not need such low threshold and I would have noisy images when I work with such low threshold. I need all images to be consistent because i am going to compare them so I may not be able to use two thresholds for these two types of images. Is there any recommendation in this case? I was thinking if changing brightness/contrast of initial image (color image) can help so that all images would have the same threshold?
You might ask what is the further analysis. I am going to count the number of pixels of one in the image to find the density of cytoskeleton.