This week we want to show what we suspect to be mitochondria and what we could do to detect them with the 3D Cell Explorer.

In a recent publication, Haseda, Keisuke, et al. (2015) were able to determine the refractive index of an isolated mitochondria (~1.41) using retardation-modulated differential interference contrast microscopy with a precision of ± 0.01. The refractive index measurement of subcellular components gives information about the structures and the functions of cells.

This value could be useful for us to detect mitochondria in a complex cell structure.

Other publications have also determined the refractive index of different subcellular structures: the nucleus (~1.39) by R.Barer, S.Joseph (1954), the cytoplasm (~1.35-1.38) studied by F.Lanni et al. (1985) and J.Beuthan et al. (1996)

Based on these results, totally automatic non-invasive detection and segmentation of the different subcellular structures would be possible with STEVE.

In figure 1 are shown cell images with distinguishable mitochondria assembly.

Figure 1. Comparison between a brown fat cell acquired with the 3D Cell Explorer (A) and an embryonic mouse fibroblast cell treated with dies (B). On the left panel of figure 1A the refractive index distribution within the cells is displayed while on the right panel the 3D reconstruction is shown. The mitochondria are digitally stained with red. On figure 1B, the mitochondria are stained in red and the nucleus in blue. The mitochondria are indicated by the green arrows. In both type of cells, we recognize the particular shape of the mitochondria assembling together in a filamentous shape. Figure 1A is courtesy of Rachana Pradhan, Laboratory of Systems Biology and Genetics, EPFL (Switzerland). Figure 1B from Zeiss.














1) Haseda, Keisuke, et al. “Significant correlation between refractive index and activity of mitochondria: single mitochondrion study.” Biomedical optics express 6.3 (2015): 859-869.

2) F. Lanni, A. Waggoner, D. Taylor, Internal reflection fluorescence microscopy, J. Cell Biol. 100 (1985) 1091–1102.

3) J. Beuthan, O. Minet, J. Helfman, G. Muller, The spatial variation of the refractive index in biological cells, Phys. Med. Biol. 41 (1996) 369–382.