2018 ISCB Art in Science Competition

Marwan Abdellah
École polytechnique fédérale de Lausanne (EPFL)

In Silico Brainbow

In silico brainbow optical section of a neocortical slice (920 × 640 × 1740 μm3) created with a virtual light-sheet fluorescence microscope (LSFM).

The simulation of the LSFM is performed on a physically-plausible basis using Monte Carlo ray tracing and geometric optics. The tissue model is reconstructed in a three-step process: 1) converting the morphological skeletons of the neurons into piecewise surface meshes that represent their membranes, 2) reconstructing a volumetric model of the tissue using solid voxelization and finally 3) tagging the neurons with the optical properties of the neocortical tissue and also the spectroscopic properties of different fluorescent dyes.

The slice is virtually-tagged with six different fluorescent proteins (GFP, CFP, eCFP, mBanana, mCherry and mPlum) and illuminated at the maximum excitation wavelength of each respective dye.