This study presents methodology for estimating biomass and lipid production by Mucor rouxii via image analysis. Morphological variations in M. rouxii in relation to its biomass and lipid production were investigated using image analysis. Two parameters were used to characterize fungal morphology: fungal area per unit volume of the culture broth (A(f); cm(2)/ml) and fungal pellet circularity skewing (S-K). These two parameters were correlated with both fungal biomass and lipid production and were used to develop an empirical model. This empirical model was further applied to estimate biomass yield and lipid production by M. rouxii under diverse culture conditions. Model predictions for fungal biomass and lipid production were in agreement with experimental results, indicating the reliability of image-based methodology. Thus, image-based methodology can be used to estimate fungal biomass and lipid production. (C) 2010, The Society for Biotechnology, japan. All rights reserved.