A new multi-resolution super-pixel based algorithm is proposed to track cell size, count and motion in Mesenchymal Stem Cells (MSCs) images. Multi-resolution super-pixels are obtained by placing varying density seeds on the image. The density of the seeds are determined according to the local high frequency components of the MSCs image. In this way a multi-resolution super-pixels decomposition of the image is obtained. A second contribution of the paper is novel decision rule for merging similar neighboring super-pixels. An algorithm based on well known wavelet decomposition is developed and applied to the histograms of neighboring super pixels to exploit similarity. The proposed algorithm is experimentally shown to be successful in segmenting and tracking cells in MSCs images.