No wonder this code runs slow. You are using dynamic memory allocation. You can get several-fold speed gain just by pre-allocation: https://www.mathworks.com/help/matlab/matlab_prog/preallocating-arrays.html. However, you don't even need a loop for this. You can do it much more efficiently like this.
I=imread('1.bmp');
[rows,columns,~]=size(I);
[c,r] = ndgrid(1:columns, 1:rows);
pix_im = [r(:) c(:)]
