A geometric phase analysis has been applied to high-resolution transmission electron microscopy images from algal cellulose microcrystals. The pictures were decomposed into images containing selectively the amplitude or phase information associated to selected Bragg reflections. Compared with I-beta (monoclinic)-rich cellulose microfibrils, I-alpha(triclinic)-rich microfibrils were found to be more heterogeneous when viewed along the H-bonding sheets. As a microfibril twist and radiation damage could not be totally ruled out as having an effect on the lattice image, this result has to be considered with care when used in order to survey the distribution of different allomorphs in a cellulose microfibril. However, the geometric phase analysis of noisy low dose high-resolution images appears as a promising new method to investigate polymer crystals and the distribution of domains having different structures or containing lattice distortions.