matplotlib imshow plots different if using colormap or RGB array

Question

I am having the following problem: I am saving 16-bit tiff images with a microscope and I need to analyze them. I want to do that with numpy and matplotlib, but when I want

Answer 1

I approached this by normalising the image by the maximum value of the given datatype, which said by DrV, for uint16 is 65535. The helper function would look something like:

def normalise_bits(img):
    bits = 1.0  # catch all
    try:
        # Test integer value, e.g. np.uint16
        bits = np.iinfo(img.dtype).max
    except ValueError:
        # Try float maximum, e.g. np.float32
        bits = np.finfo(img.dtype).max
    return (img / bits).astype(float)

Then the image can be handled by matplotlib as a float [0.0, 1.0]