Nunley, H. | bioRxiv Science

bioRxiv2023

A novel ground truth dataset enables robust 3D nuclear instance segmentation in early mouse embryos

For investigations into fate specification and cell rearrangements in time-lapse images of preimplantation embryos, automated 3D instance segmentation of nuclei and subsequent nuclear tracking are invaluable. Often, the images low signal-to-noise ratio and high voxel anisotropy and the nucleis dense packing and variable shapes limit the performance of many segmentation methods, while subsequent tracking of nuclear instances is complicated by low frame rates and sample movements. Supervised machine learning approaches can radically improve segmentation accuracy and enable easier tracking, but they often require large amounts of difficult-to-obtain annotated 3D data. Here we report a novel mouse line expressing near-infrared nuclear reporter H2B-miRFP720. H2B-miRFP720 is the longest wavelength nuclear reporter in mice and can be imaged simultaneously with other reporters with minimal overlap. We then generate a dataset, which we call BlastoSPIM, of 3D microscopy images of H2B-miRFP720-expressing embryos with ground truth for nuclear instance segmentation. Using BlastoSPIM, we benchmark the performance of seven convolutional neural networks and identify Stardist-3D as the most accurate instance segmentation method across preimplantation development. We then construct a complete pipeline for nuclear instance segmentation with our BlastoSPIM-trained Stardist-3D models and lineage tracking from the 8-cell stage to the end of preimplantation development (> 100 nuclei). Finally, we demonstrate BlastoSPIMs usefulness as pre-train data for related problems, both for a different imaging modality and for different model systems. BlastoSPIM, its corresponding Stardist-3D models, and documentation of the full associated analysis pipeline are available at: blastospim.flatironinstitute.org.

developmental biology↗

bioRxiv2021

Generation of fate patterns via intercellular forces

Studies of fate patterning during development typically emphasize cell-cell communication via diffusible signals. Recent experiments on monolayer stem cell colonies, however, suggest that mechanical forces between cells may also play a role. These findings inspire a model of mechanical patterning: fate affects cell contractility, and pressure in the cell layer biases fate. Cells at the colony boundary, more contractile than cells at the center, seed a pattern that propagates via force transmission. In agreement with previous observations, our model implies that the width of the outer fate domain depends only weakly on colony diameter. We further predict and confirm experimentally that this same width varies non-monotonically with substrate stiffness. This finding supports the idea that mechanical stress can mediate patterning in a manner similar to a morphogen; we argue that a similar dependence on substrate stiffness can be achieved by a chemical signal only if strong constraints on the signaling pathways mechanobiology are met.

biophysics↗

bioRxiv2019

Defect patterns on the curved surface of fish retinae suggest mechanism of cone mosaic formation

The outer epithelial layer of zebrafish retinae contains a crystalline array of cone photoreceptors, called the cone mosaic. As this mosaic grows by mitotic addition of new photoreceptors at the rim of the hemispheric retina, topological defects, called \"Y-Junctions\", form to maintain approximately constant cell spacing. The generation of topological defects due to growth on a curved surface is a distinct feature of the cone mosaic not seen in other well-studied biological patterns like the R8 photoreceptor array in the Drosophila compound eye. Since defects can provide insight into cell-cell interactions responsible for pattern formation, we characterize the arrangement of cones in individual Y-Junction cores as well as the spatial distribution of Y-junctions across entire retinae. We find that for individual Y-junctions, the distribution of cones near the core corresponds closely to structures observed in physical crystals. In addition, Y-Junctions are organized into lines, called grain boundaries, from the retinal center to the periphery. In physical crystals, regardless of the initial distribution of defects, grain boundaries can form via the mobility of individual particles. By imaging in live fish, we demonstrate that grain boundaries in the cone mosaic instead appear during initial mosaic formation, without requiring defect motion. Motivated by this observation, we show that a computational model of repulsive cell-cell interactions generates a mosaic with grain boundaries. In contrast to paradigmatic models of fate specification in mostly motionless cell packings, this study emphasizes the role of cell motion, guided by cell-cell interactions during differentiation, in forming biological crystals. Such a route to the formation of regular patterns may be especially valuable in situations, like growth on a curved surface, where long-ranged, elastic, effective interactions between defects can help to group them into grain boundaries.\n\nAUTHOR SUMMARYFrom hair cells in the mammalian inner ear to the bristles on a flys back, sensory cells often form precise arrays, ensuring that these cells are evenly spread out on the tissues surface. Here we consider the zebrafish cone mosaic, a crystal of cone photoreceptors in the outer retinal layer. Because the cone mosaic grows from the rim of the curved retinal surface, new rows of cones (i.e., defects) are inserted to maintain constant spacing between sensory cells. We study the spatial distribution of these defects to gain insight into how the cone pattern forms. By imaging retinae in live fish, we find that as differentiating cones are incorporated into the mosaic, defects form lines (grain boundaries) that separate mostly defect-free domains. Then, we show that a computational model based on repulsion between mobile cells during their incorporation into the mosaic generates similar grain boundaries. This study thus suggests that cell motion governed by repulsive cell-cell interactions can play an important role in establishing regular patterns in living systems.

biophysics↗