"Optical microscopy of biological samples: the importance of calibrations in holographic microscopy of bacteria infected blood samples" by Thomas Olivier

Seminar by Thomas Olivier

Abstract

We propose here a 2-step methodology based on inverse problems approach to calibrate and correct the geometrical and chromatic aberrations of the optical setup from a single hologram of a sparse biological sample. This methodology is based on a first step that jointly estimates parameters of microbeads (added to the sample) and 14 aberrations parameters (Zernike coefficients) at every wavelength. After an interpolation step on the whole field of view, the estimated aberrations and beads axial positions are taken into account in the reconstruction of the complex transmittance at focus. This reconstruction step is performed using an unsupervised, but regularized, inverse problems approach reconstruction of the whole multi-wavelength data set with a colocalization  prior. This general methodology is applied to the case of stained bacteria on blood smears. On these samples, in addition to providing a new spectral information (phase), we show interesting improvements on the image quality, which promises better discrimination between bacteria types and enhanced repeatability.

This talk is based on the PhD thesis of Dylan Brault and our recent publication in collaboration with bioMérieux (Grenoble) and BIOASTER (Lyon) :

"Multispectral in-line hologram reconstruction with aberration compensation applied to Gram-stained bacteria microscopy," D. Brault, T. Olivier, N. Faure, S. Dixneuf, C. Kolytcheff, E. Charmette, F. Soulez & C. Fournier, Scientific Reports volume 13, Article number: 14437 (2023).

This seminar will be held in English.