Tracking nano-metric particles in a biological environment is a very difficult task because of the low signal intensity and the high mobility of these small objects. The task becomes nearly impossible for classical tracking procedures when the targets are labeled with a marker that is not strictly specific, because in this case dynamic structures in the cell are also visible. To address this limitation, we propose to use a source separation technique based on sparsity principles which allows the discrimination of objects with different morphologies. We prove in a real case that tracking in the source separated images allows to track particles that interact with other sources, something which was not feasible until now. This capability opens up new perspectives for the analysis documenting intricate interactions between cellular compartments.