Enumeration of microbial cells in subsurface samples is an important baseline approach in our understanding of microbial life and ecosystems. This method has proven a challenge as non-specific fluorescent signals due to sediment particles impede efficient detection and counting of microbial cells. Therefore, the proposed travel exchange took place at Fumio Inagaki’s laboratory (JAMSTEC) in Kochi (Japan) in order to carry out computer-based automatic cell counting for gravity core sediments fixed on board during the DARCSEAS cruise in the Eastern Mediterranean Sea. This method is based on washing sediments with hydrofluoric acid, and staining with SYBR Green I in order to eliminate fluorescence of non-biological background while discriminating at the same time against background fluorescence of unspecifically stained organic material whose emission wavelengths are slightly offset from the peak of the SYBR Green I fluorescence emission window (Morono, 2009). This innovative technique will allow processing the large number of cell count samples generated during the cruise. This will in turn enable robust statistical comparison between samples as it will eliminate the bias of human counting. This information will prove useful in quantifying the microbial population in the sediment samples of the Mediterranean Sea. This travel exchange will also be very beneficial for learning this new method and training with the leading experts on this field of research.