Section: New Results

Averaging of 3D volumes and denoising for the analysis of cryo-electron tomograms

Participant : Charles Kervrann.

Trichocysts are large vesicles secreted by the ciliated protozoa, Paramecium. They are characterized by the presence of large three-dimensional crystals of proteins. Under chemical or physical stimuli, or facing a predator, trichocysts undergo an exocytosis, right after fusion of their membrane with the unicellular organism plasma membrane. The crystalline mesh changes its conformation from a condensed to an extended shape in a few milliseconds. Nowadays, cryo-electron tomography (cryo-ET) allows one to visualize those crystals and so, to analyse their three-dimensional organization. However, two main impediments remain with this method. Samples are very sensitive to electron radiation involving the spreading out of the electron dose on the whole tilt series, causing the emergence of background noise in the images. Moreover, a lack of data occurs during image acquisition, called the “missing wedge”, due to uncovered angles at the moment of the acquisition of the tilt series. After tomogram reconstruction of four trichocysts, we have tested usual denoising methods (anisotropic diffusion, Fourier coefficient thresholding) and an unpublished patch-based denoising method inspired from the nD-safir software ( 5.1 ). The denoising methods improved the alignment of different crystal sub-volumes. The sub-volume averaging allowed us to fill in partially the “missing wedge” and then, to obtain a more faithful three-dimensional crystal reconstruction [17] , [15] .

Partners: E. Pollet, A. Guesdon and D. Chrétien (UMR 6026 CNRS University of Rennes 1)