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Cryo FIB/SEM tomography and the art of digging out treasures - An exemple from biomineralization

MPI of colloïds & interfaces, Potsdam, Allemagne

mardi 26 février 2019 - 09h30 - Auditorium, IGBMC
Invité(e) par Biologie structurale intégrative, Patrick SCHULTZ

Focussed ion beam/scanning electron microscopy (FIB/SEM) based serial surface imaging (SSI) is emerging as an ideal tool in structural biology, as it allows to obtain high resolution (down to 2-3nm) tomographic datasets of relatively large volumes (up to around (100µm)3). In our group, we employ FIB/SEM both at room temperature and in cryogenic conditions to unveil the mechanisms behind the production/depsition of biological materials and tissues. Despite the acquired FIB/SEM datasets contain invaluable information to decipher these pathways and processes, these informations have to be painfully ‘mined' from the original stack of raw images. The main difficulties linked to this process are 1) the ‘clean-up' of the raw images, which suffer of artefacts and are often characterised by low signal to noise ratio, and 2) the segmentation of large portions of the tomographic volumes, which is challenged by the homogeneous brightness and the low contrast of the data. Starting from the example of a mineralising alga, Emiliania huxleyi, I will discuss these challenges and propose a pipeline for the image processing and segmentation of  (cryo)-FIB/SEM datasets.

Imprimer Envoyer

Université de Strasbourg

IGBMC - CNRS UMR 7104 - Inserm U 1258
1 rue Laurent Fries / BP 10142 / 67404 Illkirch CEDEX / France Tél +33 (0)3 88 65 32 00 / Fax +33 (0)3 88 65 32 01 / directeur.igbmc@igbmc.fr