We present a number of auto-focusing methods in lighting microscopy for its use in diatom identification. Among these, the Tenengrad method has been considered one of the best. The basic requirements for a practical auto-focusing system are speed, sharpness and robustness to noise. Recently other focus measures based on a modified Laplacian method are said to perform better than Tenengrad. We investigate two sound methods based on a modified Tenengrad and a modified Laplacian. Measurements show that they provide a reliable and suitable focus measure that outperforms similar methods. We investigate the window size analysis dependency and perform a univariate analysis on the focus measures. The focusing techniques are implemented in an automatic slide scanning system for diatom detection and identification for its use in the ADIAC project.