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We present a microfluidic device for on-chip optical analysis and characterisation of biological cells. We employ a novel waveguiding technique for detection and analysis of the cells. This waveguiding technique is particularly well suited to this since a number of unique characteristics of the optical waveguide come together to enable detailed analysis of the very low level of scattered light. We are interested in the analysis and characterisation of sub-wavelength features such as nuclei and mitochondria within living cells. Such nanoscale probing of intracellular matter promises to offer reliable diagnostic procedures for biological cells. Of particular interest are the mitochondria, since the size and number of these can provide useful information as to the health of the cell. Mitochondria are the organelles in which energy production takes place, and as such are of vital importance. Mitochondrial abnormalities are often associated with serious diseases including cancer.