arXiv subjects

Aurélien Bègue

Publications and source records attributed to Aurélien Bègue.

3 recordsLinked to original sources

arXiv2023

Imaging across multiple spatial scales with the multi-camera array microscope

This article experimentally examines different configurations of a novel multi-camera array microscope (MCAM) imaging technology. The MCAM is based upon a densely packed array of "micro-cameras" to jointly image across a large field-of-view at high resolution. Each micro-camera within the array images a unique area of a sample of interest, and then all acquired data with 54 micro-cameras are digitally combined into composite frames, whose total pixel counts significantly exceed the pixel counts of standard microscope systems. We present results from three unique MCAM configurations for different use cases. First, we demonstrate a configuration that simultaneously images and estimates the 3D object depth across a 100 x 135 mm^2 field-of-view (FOV) at approximately 20 um resolution, which results in 0.15 gigapixels (GP) per snapshot. Second, we demonstrate an MCAM configuration that records video across a continuous 83 x 123 mm^2 FOV with two-fold increased resolution (0.48 GP per frame). Finally, we report a third high-resolution configuration (2 um resolution) that can rapidly produce 9.8 GP composites of large histopathology specimens.

eess.IV↗

arXiv2023

Parallelized computational 3D video microscopy of freely moving organisms at multiple gigapixels per second

To study the behavior of freely moving model organisms such as zebrafish (Danio rerio) and fruit flies (Drosophila) across multiple spatial scales, it would be ideal to use a light microscope that can resolve 3D information over a wide field of view (FOV) at high speed and high spatial resolution. However, it is challenging to design an optical instrument to achieve all of these properties simultaneously. Existing techniques for large-FOV microscopic imaging and for 3D image measurement typically require many sequential image snapshots, thus compromising speed and throughput. Here, we present 3D-RAPID, a computational microscope based on a synchronized array of 54 cameras that can capture high-speed 3D topographic videos over a 135-cm^2 area, achieving up to 230 frames per second at throughputs exceeding 5 gigapixels (GPs) per second. 3D-RAPID features a 3D reconstruction algorithm that, for each synchronized temporal snapshot, simultaneously fuses all 54 images seamlessly into a globally-consistent composite that includes a coregistered 3D height map. The self-supervised 3D reconstruction algorithm itself trains a spatiotemporally-compressed convolutional neural network (CNN) that maps raw photometric images to 3D topography, using stereo overlap redundancy and ray-propagation physics as the only supervision mechanism. As a result, our end-to-end 3D reconstruction algorithm is robust to generalization errors and scales to arbitrarily long videos from arbitrarily sized camera arrays. The scalable hardware and software design of 3D-RAPID addresses a longstanding problem in the field of behavioral imaging, enabling parallelized 3D observation of large collections of freely moving organisms at high spatiotemporal throughputs, which we demonstrate in ants (Pogonomyrmex barbatus), fruit flies, and zebrafish larvae.

physics.optics↗

arXiv2011

Shaped two-photon excitation deep inside scattering tissue

Light is the tool of the 21st century. New photosensitive tools offer the possibility to monitor and control neuronal activity from the sub-cellular to the integrative level. This ongoing revolution has motivated the development of new optical methods for light stimulation. Among them, it has been recently demonstrated that a promising approach is based on the use of wavefront shaping to generate optically confined extended excitation patterns. This was achieved by combining the technique of temporal focusing with different approaches for lateral light shaping including low numerical aperture Gaussian beams, holographic beams and beams created with the generalized phase contrast mthod. What is needed now is a precise characterization of the effect of scattering on hese different methods in order to extend their use for in depth excitation. Here we present a theoretical and experimental study on the effect of scattering on the propagation of wavefront shaped beams. Results from fixed and acute cortical slices show that temporally focused spatial patterns are extremely robust against the effects of scattering and this permits their three-dimensional confinement for depths up to 550 μm.

physics.optics↗