Measuring chromatin fluorescence
Goal: we want to quantify the amount of a particular protein (red fluorescence) localized on the centromeres (green) versus the rest of the chromosome (blue).
The main challenge here is the uneven illumination, which makes isolating the chromosomes a struggle.
Let's separate the channels so we can work on each individually.
Getting the centromeres is easy because the signal is so clean:
But getting the chromosomes is not so easy:
Let's try using an adaptive threshold:
Not only is the uneven illumination a problem, but there seem to be some artifacts due to the illumination pattern!
Exercise: Can you think of a way to fix this?
(Hint: in addition to everything you've learned so far, check out skimage.morphology.remove_small_objects
)
Now that we have the centromeres and the chromosomes, it's time to do the science: get the distribution of intensities in the red channel using both centromere and chromosome locations.