Biology subjects

Musy, M.

Publications and source records attributed to Musy, M..

5 recordsLinked to original sources

bioRxiv2025

3D Mapping of Intact Ovaries Reveals the Aging Dynamics of the Ovarian Reserve

Female fertility depends on a finite pool of oocytes that depletes during aging, yet the spatiotemporal dynamics of this depletion remain poorly understood. Traditional methods obscure the 3D architecture of the ovary, limiting quantitative insights. Here, we combine light-sheet microscopy, artificial intelligence (AI)-driven segmentation, and mathematical modeling to map over 85,000 oocytes in whole-ovaries across the reproductive lifespan in mouse. We find that newly activated oocytes represent a fixed fraction of the ovarian reserve, despite an age-related decline in total oocyte numbers. Spatial analysis revealed that oocytes are enriched along the lateral ovarian axis, and local oocyte density positively correlates with activation. We also uncover a bimodal distribution of oocyte sizes, suggesting a bottleneck during oogenesis. Finally, a differential equation-based model captures the kinetics of oocyte activation and loss. Our findings establish a quantitative framework for understanding ovarian aging and suggest that an organ-scale regulatory mechanism coordinates the age-related decline in oocyte numbers.

cell biology↗

bioRxiv2025

LimbLab: Pipeline for 3D Analysis and Visualisation of Limb Bud Gene Expression

MotivationAlthough some aspects of limb development can be treated as a 2D problem, a true understanding of the morphogenesis and patterning requires 3D analysis. Since the data on gene expression patterns are largely static 3D image stacks, a major challenge is an efficeint pipeline for staging each data-set, and then aligning and warping the data into a standard atlas for convenient visualisation. ResultsWe present a novel bioinformatic pipeline tailored for 3D visualization and analysis of developing limb buds. The pipeline integrates key steps such as data acquisition, volume cleaning, surface extraction, staging, alignment, and advanced visualization techniques. Its modular design allows researchers to customize workflows while maintaining compatibility with tools such as Fiji and Vedo. Our results highlight the pipelines effectiveness in managing complex 3D gene expression data, enhancing the accuracy and reproducibility of limb development studies. Availability and ImplementationLimbLab is released under the MIT license. The pipeline is implemented in Python and is available as an open-source package. It can be easily installed via pip and is accompanied by comprehensive documentation (https://limblab.embl.es/) to support users at various levels of expertise. The pipeline can be accessed and downloaded at https://github.com/LauAvinyo/limblab.

bioinformatics↗

bioRxiv2024

Cell 3D Positioning by Optical encoding (C3PO) and its application to spatial transcriptomics

Current state-of-the-art spatial omics approaches suffer from the drawback that they are tissue section-based and thus inherently 2-dimensional. A full understanding of biological processes will only be possible when such data is available in 3-dimensions (3D). Here, we introduce Cell 3D Positioning by Optical encoding (C3PO) - the first technique capable of reconstructing the 3D positions of cells in a tissue, after they have been fully dissociated for single-cell omics analysis. It imposes a Cartesian coordinate system of positions on the tissue and cells of interest, before dissociation. This is created by multiple orthogonal spatial gradients of active fluorophores, carefully shaped by a 3D bleaching method, such that each position in the tissue is encoded by a unique fluorescent address. Upon dissociation of the tissue the fluorescent addresses of the cells can be read via an appropriate device (such as a FACS machine) to computationally reconstruct the tissue in 3D, before omics are performed downstream. Here, we show two proof-of-principle results for C3PO. First, pure C3PO without omics, to reconstruct the 3D geometry of a developing mouse limb bud. Second, an application of C3PO to spatial transcriptomics, revealing the expression patterns of 73 genes with interesting gene expression patterns in the developing limb.. C3PO is a genuinely novel approach to reconstruct the original 3D positions of cells in a tissue after dissociation. Combined with transcriptomics, it can play a significant role in the study of any tissue or organ in which 3D structure and geometry is important, such as developmental biology, cancer biology and neuroscience. It is not an omics technique per se, and in the future could be combined with the growing family of other omics technologies. One sentence summaryC3PO is a novel optical technique that can preserve the 3D positional coordinates of cells after tissue dissociation, enabling a radically new approach to spatial transcriptomics.

molecular biology↗

bioRxiv2021

4D reconstruction of developmental trajectories using spherical harmonics

Although the full embryonic development of species such as Drosophila and zebrafish can be 3D imaged in real time, this is not true for mammalian organs, as normal organogenesis cannot be recapitulated in vitro. Currently available 3D data is therefore ex vivo images which provide only a snap shot of development at discrete moments in time. Here we propose a computer-based approach to recreate the continuous evolution in time and space of developmental stages from 3D volumetric images. Our method uses the mathematical approach of spherical harmonics to re-map discrete shape data into a space in which facilitates a smooth interpolation over time. We tested our approach on mouse limb buds (from E10 to E12.5) and embryonic hearts (from 10 to 29 somites). A key advantage of the method is that the resulting 4D trajectory takes advantage of all the available data (i.e. it is not dominated by the choice of a few "ideal" images), while also being able to interpolate well through time intervals for which there is little or no data. This method not only provides a quantitative basis for validating predictive models, but it also increases our understanding of morphogenetic processes. We believe this is the first data-driven quantitative 4D description of limb morphogenesis.

developmental biology↗

bioRxiv2020

Cellular mechanisms of chick limb bud morphogenesis

Although some of the molecular pathways involved in limb bud morphogenesis have been identified, the cellular basis of the process is not yet understood. Proposed cell behaviours include active cell migration and oriented cell division, but ultimately, these questions can only be resolved by watching individual mesenchymal cells within a completely normal developmental context. We developed a minimally-invasive in ovo two-photon technique, to capture high quality time-lapse sequences up to 100 microns deep in the unperturbed growing chick limb bud. Using this technique, we characterized cell shapes and other oriented behaviours throughout the limb bud, and found that cell intercalation drives tissue movements, rather than oriented cell divisions or migration. We then developed a 3D cell-based computer simulation of morphogenesis, in which cellular extensions physically pull cells towards each other, with directional bias controlled by molecular gradients from the ectoderm (Wnts) and the Apical Ectodermal Ridge (FGFs). We defined the initial and target shapes of the chick limb bud in 3D by OPT scanning, and explored which orientations of mesenchymal intercalation correctly explain limb morphogenesis. The model made a couple of predictions: Firstly, that elongation can only be explained when cells intercalate along the direction towards the nearest ectoderm. This produces a general convergence of tissue towards the central proximo-distal (PD) axis of the limb, and a resultant extension of the tissue along the PD axis. Secondly, the correct in silico morphology can only be achieved if the contractile forces of mesenchymal cells in the very distal region (under the Apical Ectodermal Ridge) have shorter life times than in the rest of the limb bud, effectively making the tissue more fluid by augmenting the rate of cell rearrangement. We argue that this less-organised region of mesenchyme is necessary to prevent PD-oriented intercalation events in the distal tip that would otherwise inhibit outgrowth.

developmental biology↗