Biology subjects

Wong, M.-K.

Publications and source records attributed to Wong, M.-K..

6 recordsLinked to original sources

bioRxiv2024

EmbSAM: Cell boundary localization and Segment Anything Model for fast images of developing embryos

Cellular shape dynamics are critical for understanding cell fate determination and organogenesis during development. However, fluorescence live-cell images of cell membranes frequently suffer from a low signal-to-noise ratio, especially during long-duration imaging with high spatiotemporal resolutions. This is caused by phototoxicity and photobleaching, which limit laser power and hinder effective time-lapse cell shape reconstruction, particularly in rapidly developing embryos. Here, we devised a new computational framework, EmbSAM, that incorporates a deep-learning-based cell boundary localization algorithm and the Segment Anything Model. EmbSAM enables accurate and robust three-dimensional (3D) cell membrane segmentation for roundworm Caenorhabditis elegans embryos imaged every 10 seconds. The cell shape data prior to gastrulation quantitatively characterizes a series of cell-division-coupled morphodynamics associated with cell position, cell identity, lineage, and fate, and can be accessed locally and online. The framework also exhibits potential in segmenting and quantifying the fluorescence labeling various cell-membraned-attached molecules in both wild-type and RNAi-treated embryos.

bioinformatics↗

bioRxiv2023

Quantitative cell morphology in C. elegans embryos reveals regulations of cell volume asymmetry

The dynamics of cellular morphology throughout development are crucial for morphogenesis and organogenesis, yet their systematic characterization remains a significant challenge. By integrating both nuclear position and advanced cell membrane labeling, we develop a novel method that enables the segmentation of surfaces for over 95% of cells produced during Caenorhabditis elegans embryogenesis. With this method, we segment eight wild-type and four perturbed embryos. The output, including cell identity, shape, volume, surface and contact area, can be visualized using our custom software. We demonstrate that signaling interactions, such as Notch and Wnt, regulate not only the asymmetry of cell fate but also the asymmetry of cell volume in conjunction with mechanical compression. Furthermore, we find that the asymmetries of fate and volume are generally interconnected. ONE SENTENCE SUMMARYSystematic quantification of cell morphology with resolved cell lineage and cell fate in developing C. elegans embryo uncovers multimodal regulations of cell size. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=190 SRC="FIGDIR/small/567849v1_ufig1.gif" ALT="Figure 1"> View larger version (114K): org.highwire.dtl.DTLVardef@1b7d0fforg.highwire.dtl.DTLVardef@fa28b1org.highwire.dtl.DTLVardef@185a0deorg.highwire.dtl.DTLVardef@478a2_HPS_FORMAT_FIGEXP M_FIG C_FIG Potential Cover/Featured Image: Smiling "ghost" face of C. elegans embryo. Center: shown are skins (colored in red, dorsal view with anterior to the bottom) of a 400-celled C. elegans embryo. Cells not covered by the skins are colored in gray, green, blue, and transparent yellow, respectively. Internal and external circles: confocal fluorescence images (GFP for cell nucleus and mCherry for cell membrane) and reconstructed cell morphologies of the C. elegans embryo from the 2- to 550-cell stages respectively, connected with images of a C. elegans adult expressing the same markers.

developmental biology↗

bioRxiv2020

Computable Early C. elegans Embryo with a Data-driven Phase Field Model

Morphogenesis is a precise and robust dynamic process during metazoan embryogenesis, consisting of both cell proliferation and cell migration. Despite the fact that much is known about specific regulations at the molecular level, how cell proliferation and migration together drive the morphogenesis at the cellular and organismic levels is not well understood. Here, using Caenorhabditis elegans as the model animal, we present a data-driven phase field model to compute the early embryonic morphogenesis within a confined eggshell. By using three-dimensional time-lapse cellular morphological information generated by imaging experiments to set the model parameters, we can not only reproduce the precise evolution of cell location, cell shape and cell-cell contact relationship in vivo, but also reveal the critical roles of cell division and cell-cell attraction in governing the early development of C. elegans embryo. In brief, we provide a generic approach to compute the embryonic morphogenesis and decipher the underlying mechanisms.

systems biology↗

bioRxiv2019

Establishment of morphological atlas of Caenorhabditis elegans embryo with cellular resolution using deep-learning-based 4D segmentation

Cell lineage consists of cell division timing, cell migration and cell fate, which are highly reproducible during the development of some nematode species, including C. elegans. Due to the lack of high spatiotemporal resolution of imaging technique and reliable shape-reconstruction algorithm, cell morphology have not been systematically characterized in depth over development for any metazoan. This significantly inhibits the study of space-related problems in developmental biology, including cell segregation, cell-cell contact and cell shape change over development. Here we develop an automated pipeline, CShaper, to help address these issues. By quantifying morphological parameters of densely packed cells in developing C. elegans emrbyo through segmentation of fluorescene-labelled membrance, we generate a time-lapse framework of cellular shape and migration for C. elegans embryos from 4-to 350-cell stage, including a full migration trajectory, morphological dynamics of 226 cells and 877 reproducible cell-cell contacts. In combination with automated cell tracing, cell-fate associated cell shape change becomes within reach. Our work provides a quantitative resource for C. elegans early development, which is expected to facilitate the research such as signaling transduction and cell biology of division.

developmental biology↗

bioRxiv2019

System-Level Quantification and Phenotyping of Early Embryonic Morphogenesis of Caenorhabditis elegans

Cell lineage consists of cell division timing, cell migration and cell fate, and is highly conserved during development of nematode species. An outstanding question is how differentiated cells are genetically and physically regulated in order to migrate to their precise destination among individuals. Here, we first generated a reference embryo using time-lapse 3 dimensional images of 222 wild-type C. elegans embryos at about 1.5-minute interval. This was achieved by automatic tracing and quantitative analysis of cellular phenotypes from 4- to 24-cell stage, including cell cycle duration, division orientation and migration trajectory. We next characterized cell division timing and cell kinematic state, which suggests that eight groups of cells can be clustered based on invariant and distinct division sequence. Cells may still be moving while others start to divide, indicating strong robustness against motional noise in developing embryo. We then devised a system-level phenotyping method for detecting mutant defect in global growth rate, cell cycle duration, division orientation and cell arrangement. A total of 758 genes were selected for perturbation by RNA interference followed by automatic phenotyping, which suggests a cryptic genetic architecture coordinating early morphogenesis spatially and temporally. The high-quality wild-type reference supports a conceptual close-packing model for cell arrangement during 4- to 8-cell stage, implying fundamental mechanical laws regulating the topological structure of early C. elegans embryo. Also, we observed a series of remarkable morphogenesis phenomena such as induced defect or recovery from defect in mutant embryo. To facilitate use of this quantification system, we built a software named STAR 1.0 for visualizing the wild-type reference and mutant phenotype. It also allows automatic phenotyping of new mutant embryo. Taken together, we not only provide a statistical wild-type reference with defined variability, but also shed light on both genetic and physical mechanisms coordinating early embryonic morphogenesis of C. elegans. The statistical reference permits a sensitive approach for mutant phenotype analysis, with which we phenotype a total of 1818 mutant embryos by depletion of 758 genes.\n\nHighlights & Graphical Abstract[bullet] Spatial-Temporal Wild-Type Reference for Early Embryonic Morphogenesis of C. elegans\n[bullet]Variability (Noise) of Division Timing, Division Orientation and Cell Arrangement\n[bullet]A Conceptual Close-Packing Model for Cell Arrangement Up to 8-Cell Stage\n[bullet]Quantitative Phenotyping Methods at Embryo and Cellular Level\n[bullet]Cellular Phenotypes of 1818 Mutant Embryos (758 Genes) Before Gastrulation\n[bullet]Categorized Phenotypes upon Gene Perturbation\n\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC=\"FIGDIR/small/776062v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (37K):\norg.highwire.dtl.DTLVardef@2ec730org.highwire.dtl.DTLVardef@11732deorg.highwire.dtl.DTLVardef@ccbf4org.highwire.dtl.DTLVardef@2218d1_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2018

Establishment of signaling interactions with cellular resolution for every cell cycle of embryogenesis

Intercellular signaling interaction plays a key role in breaking fate symmetry during animal development. Identification of the signaling interaction at cellular resolution is technically challenging, especially in a developing embryo. Here we develop a platform that allows automated inference and validation of signaling interaction for every cell cycle of C. elegans embryogenesis. This is achieved by generation of a systems-level cell contact map that consists of 1,114 highly confident intercellular contacts by modeling analysis and is validated through cell membrane labeling coupled with cell lineage analysis. We apply the map to identify cell pairs between which a Notch signaling interaction takes place. By generating expression patterns for two ligands and two receptors of Notch signaling pathway with cellular resolution using automated expression profiling technique, we are able to refine existing and identify novel Notch interactions during C. elegans embryogenesis. Targeted cell ablation followed by cell lineage analysis demonstrates the roles of signaling interactions over cell division in breaking fate symmetry. We finally develop a website that allows online access to the cell-cell contact map for mapping of other signaling interaction in the community. The platform can be adapted to establish cellular interaction from any other signaling pathways.

cell biology↗