Biology subjects

Sapede, D.

Publications and source records attributed to Sapede, D..

3 recordsLinked to original sources

bioRxiv2024

μPIX: Leveraging Generative AI for Enhanced, Personalized and Sustainable Microscopy

Fluorescence microscopy is a critical tool in bio-cellular research, enabling the visualization of biological tissues and cellular structures. However, the inevitable aging of microscopes can degrade their performance posing challenges for long-term scientific investigations. In this study, we introduce {micro}PIX, a personalized deep learning workflow based on a Generative Adversarial Network (GAN) utilizing a Pix2Pix architecture. The network is trained in a supervised manner to denoise images, optimize pre-processing for binary segmentation, and compensate for equipment aging. Our results, evaluated using standard image quality and binary segmentation metrics, demonstrate that {micro}PIX outperforms popular deep learning architectures based on convolutional auto-encoder networks for similar tasks. Additionally, our generative model effectively rejuvenates older detectors to perform on par with newer ones, not only by improving image quality but also by preserving resolution in depth and maintaining a near-linear response between original and generated images in terms of pixel intensity (crucial for quantitative imaging). These findings suggest that generative deep learning approaches can significantly contribute to more sustainable, cost-effective microscopy, fostering continued innovation and discovery in biological research.

bioinformatics↗

bioRxiv2022

Analysis of photoentrainment in the diurnal zebrafish suggests a profound divergence with nocturnal rodents

The eye is instrumental for controlling circadian rhythms in mice and human. Here, we address the conservation of this function in the zebrafish, a diurnal vertebrate. Using lakritz (lak) mutant larvae, which lack retinal ganglion cells (RGCs), we show that while a functional eye contributes to masking, it is largely dispensable for the establishment of circadian rhythms of locomotor activity. Furthermore, the eye is dispensable for the induction of a phase delay following a pulse of white light at CT 16 but contributes to the induction of a phase advance upon a pulse of white light at CT21. Melanopsin photopigments are important mediators of photoentrainment, as shown in nocturnal mammals. One of the zebrafish melanopsin genes, opn4xa, is expressed in RGCs but also in photosensitive projection neurons in the pineal gland. Pineal opn4xa+ projection neurons function in a LIGHT ON manner in contrast to other projection neurons which function in a LIGHT OFF mode. We generated an opn4xa mutant in which the pineal LIGHT ON response is impaired. This mutation has no effect on masking and circadian rhythms of locomotor activity, or for the induction of phase shifts, but slightly modifies period length when larvae are subjected to constant light. Finally, analysis of opn4xa;lak double mutant larvae did not reveal redundancy between the function of the eye and opn4xa in the pineal for the control of phase shifts after light pulses. Our results support the idea that the eye is not the sole mediator of light influences on circadian rhythms of locomotor activity and highlight differences in the circadian system and photoentrainment of behaviour between different animal models. Author summaryExperiments performed in mice have established a crucial role for the eye in general and melanopsin expressing cells in particular in the control of circadian rhythms most notably during photoentrainment, by which circadian rhythms adapt to a changing light environment. In marked contrast to this, we show that in zebrafish the eye and photosensitivity dependent on one of the melanopsin genes, opn4xa, which is expressed in both the eye and the pineal gland, are largely dispensable for correct circadian rhythms. These results provide insight that the light sensors orchestrating circadian rhythms of locomotor activity are different between animal models supporting that vertebrates might employ different molecular/cellular circuits for photoentrainment of behaviour depending on their phylogeny and/or temporal niche.

neuroscience↗

bioRxiv2019

A novel subtype of pineal projection neurons expressing melanopsin share a common developmental program with classical projection neurons

The zebrafish pineal organ is a photoreceptive structure containing two main neuronal populations (photoreceptors and projections neurons). Here we describe a new pineal cell type that harbors both characteristics of projection neurons and photoreceptors. Indeed, a subpopulation of projection neurons expresses the melanopsin gene opn4xa suggesting photoreceptive properties. This population of hybrid cell fates, share a similar behaviour regarding dependency for BMP and Notch signalling pathways with classical non-photosensitive projection neurons (PNs) suggesting they are closer to the PN population. We describe two distinct types of activity within PNs: an achromatic LIGHT OFF activity in opn4xa- PNs and a LIGHT ON activity elicited by green and blue light in opn4xa+ PNs. Altogether the discovery and characterization of opn4xa+ PNs suggest a previously unanticipated heterogeneity in the projection neuron population.

neuroscience↗