I am new to cell image processing. I have a dataset consisting of plates of images. I used an existing ML based model to extract image features, then I found batch effects among those features.
After reading a very nice paper, I decided to try Relative Normalization to remove batch effects. Fortunately, there are untreated control cells in each plate, so I used them as my normalizing population and computed their feature mean and standard deviation for each plate.
Interestingly, the standard deviation of some normalizing population’s features in one plate is 0, where treated cells have non-zero values. I am not sure how to carry on the normalization. Perhaps I could use the mean and standard deviation of all cells in that plate instead of only untreated cells, for those features?
Any suggestions will be appreciated