loss of cells after watershed transformation

I have the following figure of a population of cells. The dark spots are cell nuclei. I'm trying to segment these cells. As you can tell that some cells are connected and I want to apply watershed transformation to segment these cells.

This is what I do

I = imread('testFigure.gif'); bw = imbinarize(watershed(Im)); imwrite(bw,'ProcessedFigure.gif');

The processed figure looks like this

Though those connected cells are successfully separated as expected, but I lost many cells in the left of the figure somehow. I'm trying to understand the reason for this. Many thanks for any help.

Rui

Answer 1

[Sanjana Ramakrishnan]

Since the output image of 'watershed' method is not uniformly illuminated, use the 'adaptive' paramater of 'imbinarize' method as below to display the cells on the left hand side of the original image:

>>I = imread('testFigure.gif');

>>bw = imbinarize(watershed(I),'adaptive');

>>imwrite(bw,'ProcessedFigure.gif');

Refer the below link for more information:

https://www.mathworks.com/help/images/ref/imbinarize.html

[ruima86]

Thanks! It works