Manual Count Threshold Explanation


I’m working with an 8-bit grayscale image (0-255) and I want to threshold it so all pixels below 40 intensity are 0 and the foreground is 255 so I can find the foreground.

I’m using the Apply Threshold Module and setting it to output Binary and thresholding method to Manual.

For the Manual Threshold number it gives me an option of 0-1. I’m not sure what this number represents. Is it a percentage threshold based on 0-255? For example, 0.1 = 10% threshold so 25.5 intensity pixels are removed?

Or does it represent something else?

Thanks in advance.


Hi Mike,

CellProfiler internally scales all images to the range of 0 to 1, based on the bit-depth of the input image format, for consistency between formats. In your case, for your 8-bit images, the value 255 is scaled to 1. So you are correct in saying that a manual threshold of 0.1 would correspond to pixels greater than 25.5 being assigned as foreground.