Purification of waste water is commonly done using the activated sludge process. The ratio of the activated sludge flocs and filamentous bacteria play a key role in the purification process of waste water. The sludge bulking or filamentous bulking is a common problem in activated sludge plants that prevents flocs to settle down. Digital imaging techniques can play an important role in monitoring activated sludge flocs and filaments in waste water treatment plants (WWTPs). In this paper, an algorithm to segment the flocs and the filaments of the microscopic sludge images captured at 4 times magnification in brightfield microscopy has been proposed. Morphological parameters, like, compactness, roundness, convexity, equivalent diameter are analyzed. Comparison with laser particle size analysis method has been done for the interpretation of the imaging results. © 2014 IEEE.