CNN-3d-lensfree

Published : 27 February 2019

At CEA-Leti, we are developing lensfree microscopy for the monitoring of cell culture. This technique overpass several limits of conventional microscopy (compactness, field of view, quantification, etc.). Recently we showed, for the first time, 3D+time acquisitions of 3D cell culture with a lens-free microscope. We observed cells without any labelling within the volume as large as several cubic millimeters over several days. This new mean of microscopy allowed us to observe a broad range of phenomena only present in 3D environments. However, two drawbacks are still present on the microscope prototype: a long reconstruction time (>1 hour/frame) and the reconstructed volumes present artefacts owing to the limited number of angular acquisitions. The thesis work will focus on the ability of deep learning technologies to overcome the above-mentioned limitations. Basically, a convolutional neural network will be trained on the basis of simulated 3D cell culture volume (ground truth) and simulated response of our current 3D lensfree microscope (input). This approach is expected to accelerate the reconstruction process and to allow full 3D reconstructions. Yet it poses two scientific questions: are simulated data pertinent to train a neural network and how can we assess the quality of 3D reconstruction obtained through a neural network?

Profile of the candidate sought:

– Engineering degree in applied mathematics or physical sciences.

– Strong knowledge in image processing with skills in deep learning.

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