Maybe too old question, can be done with ease using opencv

cv2.addWeighted(img1, alpha, img2, beta, gamma)
#setting alpha=1, beta=1, gamma=0 gives direct overlay of two images

Documentation link

I would be inclined to paste Si and Al images using a mask so that they only affect the SEM image where they are coloured and not where they are black/grey - else you will tend to reduce the contrast of your base image:

from PIL import Image

# Load images
sei = Image.open('sei.jpg')
si = Image.open('si.jpg')
al = Image.open('al.jpg')

# Make mask which only allows coloured areas to show
siMask = si.convert('L')
siMask.save('DEBUG-siMask.jpg')

# Paste Si image over SEM image with transparency mask
sei.paste(si, siMask)

# Make mask which only allows coloured areas to show
alMask = al.convert('L')
alMask.save('DEBUG-alMask.jpg')

# Paste Al image over SEM image with transparency mask
sei.paste(al, alMask)
sei.save('result.png')

DEBUG-siMask.jpg

DEBUG-alMask.jpg

result.jpg

Note that you could enhance the masks before use - for example you could median filter to remove small speckles, or you could contrast stretch to make the magenta/yellow shading come out more or less solid. For example, you can see the yellow is more solid than the magenta, which is because the yellow mask is brighter, so you could threshold the magenta mask to make it pure black and white which would make the magenta come out solid.

So, I median-filtered out the speckles and changed the masking so that coloured areas are 50% transparent like this:

#!/usr/bin/env python3

from PIL import Image, ImageFilter

# Load images
sei = Image.open('sei.jpg')
si = Image.open('si.jpg')
al = Image.open('al.jpg')

# Make mask which only allows coloured areas to show
siMask = si.convert('L')
# Median filter mask to remove small speckles
siMask = siMask.filter(ImageFilter.MedianFilter(5))
# Threshold mask and set opacity to 50% for coloured areas
siMask = siMask.point(lambda p: 128 if p > 50 else 0)
siMask.save('DEBUG-siMask.jpg')

# Paste Si image over SEM image with transparency mask
sei.paste(si, siMask)

# Make mask which only allows coloured areas to show
alMask = al.convert('L')
# Median filter mask to remove small speckles
alMask = alMask.filter(ImageFilter.MedianFilter(5))
# Threshold mask and set opacity to 50% for coloured areas
alMask = alMask.point(lambda p: 128 if p > 50 else 0)
alMask.save('DEBUG-alMask.jpg')

# Paste Al image over SEM image with transparency mask
sei.paste(al, alMask)
sei.save('result.jpg')

That gives these masks and results: