Integrated quantitative imaging and biomechanical modeling of early gastrulation in C. elegans

Integrated quantitative imaging and biomechanical modeling of early gastrulation in C. elegans This repository contains the data associated with the paper "Integrated quantitative imaging and biomechanical modeling of early gastrulation in C. elegans". It includes raw microscopy, segmented 3D meshes, extensive geometric and protein analysis, simulation data, and analysis notebooks. The source code for running the biomechanical simulations and notebooks can be found at:https://bitbucket.org/pgmsembryogenesis/gastsim/src/master Folder structure /analysis: Contains processed data derived from the segmented meshes. /geom: Geometric measurements like cell volumes, contact areas, and curvatures. /protein: Cortical protein quantification and distribution statistics. /polarity: Data related to the spatial polarization of proteins, including profiles for kymographs. /microscopy: Raw image stacks from confocal microscopy. /notebooks: Jupyter notebooks and Python scripts used to analyze data and generate the visualizations presented in the paper. /segmentations: 3D segmented embryo meshes stored in VTP file format. /simulation: Output data from the biomechanical simulations, alongside the scenario mapping. /src: Snapshot of the simulation source code (gastsim) at the time of zenodo submission. README.md: This file. Appendix: Data file column descriptions This section provides a detailed description of the columns for each data file. Analysis data analysis/geom/anchor_points.pkl Stores orientation data for each replicate, defining the embryonic (AP, DV, LR) and ingression (Xe, Ye, Ze) axes. Column Name Description cell_name Identifier for an axis (e.g., 'AP') or a cell used as an anchor point. centroid_x, _y, _z Positional vector for the axis or anchor point. tc_level_1 Unique replicate identifier (e.g., 'hmr05'). analysis/geom/contact_areas.pkl Contains cell-cell contact information. Column Name Description area Contact area in um2. area_norm Area normalized by embryo size. t_E, t_EMS Time in minutes relative to the E or EMS cell division. filter A boolean flag to exclude invalid data points from analysis. analysis/geom/curvatures.pkl Surface curvature data for cell-cell interfaces. A contactidCanonical equal to parentIndexCanonical indicates a free (apical) surface. Column Name Description parentIndexCanonical Canonical ID for the primary cell. contactidCanonical Canonical ID for the contacting cell. curvatures Curvature calculated as 1/R. curvature_centered Curvature of a central patch of the contact area for more stable measurements. analysis/geom/division_angles.pkl Describes the orientation of cell divisions. Column Name Description cell The mother cell. normal-x, _y, _z Normal vector of the division plane. DV_degrees, AP_degrees, LR_degrees Division angles in degrees relative to the embryonic axes. apical_degrees Division angle in degrees relative to the apical surface. Xe_degrees, Ye_degrees, Ze_degrees Division angles in degrees relative to the ingression axes. analysis/geom/ingression_metrics.pkl Tracks ingression of the endodermal precursor cells, Ea and Ep. Column Name Description dist_end_pos The final ingression distance at the last timepoint. IngressionDist Ingression distance along the ingression axis at the given timepoint. sphericity A measure of how spherical the cell is (1 = perfect sphere). avg_curvature The average curvature of the cell surface. t_E_norm Time from E-cell division, normalized across replicates. analysis/protein/prot_cell.pkl & analysis/protein/prot_surf.pkl Cortical protein data at the whole-cell or cell-surface (interface) level. Column Name Description prot_sig Normalized and corrected protein signal intensity used in analysis. prot_sig_raw Raw signal intensity from microscopy. prot_com Center of Mass distance. Quantifies the spatial asymmetry of the protein distribution. prot_moi Moment of Inertia. Indicates if protein is concentrated centrally (<1) or spread to the periphery (>1). prot_com_raw, prot_moi_raw Raw, unnormalized values for prot_com and prot_moi. prot_pc1_x, _y, _z The first principal component vector of the protein distribution. explainedVariance The variance explained by the first principal component. analysis/protein/prot_cell_stats.pkl & analysis/protein/prot_surf_stats.pkl Statistical analysis (mean, sem, p-value) of the protein metrics at the cell and surface level. Column Name Description prot_sig, prot_com, prot_moi These columns are used as category headers for the stats. mean Mean value of the metric. sem Standard error of the mean. pvalue P-value from the statistical test. effectSize The calculated effect size. analysis/protein/prot_prof.pkl (and related files) Contains protein profiles used to generate kymographs. Column Name Description protein The averaged protein signal for a given spatial bin in the profile. prot_norm The protein signal normalized to represent a percentage weight within the profile. prot The type of protein signal (e.g., 'myosin_predict_t'). '_predict_t' indicates correction for time and depth. cut The distance bin of the profile. distance The type of axis used for the profile (e.g., 'Eap_dist' for the Ea-Ep interface). Simulation data Data is stored in /simulation/group{ID}/group_agg.pickle. This is a dictionary where keys are filenames and values are pandas DataFrames. simulation_groups.csv Links simulation groups to specific scenarios described in the paper. Column Name Description scenario_id Identifier for the simulation scenario. name_matplotlib Formatted scenario name for use in plots. groups Space-separated list of simulation group IDs associated with this scenario. comment Additional notes or details about the scenario configuration. label Short label for the scenario. gastsim.pickle (Metadata) Column Name Description segrepl The source replicate ID (e.g., '4' for 'crm04'). group_id The simulation group identifier. simtype Active events in the simulation (e.g., 'AcCd' for Apical constriction + Cell division). wt Adhesion energy, as a relative scalar to surface tension. apical_tension_driver The metric tracked by the apical tension controller (e.g., 'apicalArea'). mitotic_tension_factor Surface tension during mitosis, relative to interphase surface tension. visco_cortex, visco_liq, cell_cell_friction Key mechanical viscosity and friction parameters. traction_force Strength of corrective traction forces, if applied. run_success Boolean indicating if the simulation completed without errors. simapicaltension.txt Time-series log of ingression metrics and applied tension for Ea and Ep during simulation. Column Name Description cell The cell being logged ('Ea' or 'Ep'). sim_time The time point within the simulation. ingressionDist, apicalArea, curvatures The value of the metric at sim_time. ..._target The target value for the metric, interpolated from segmentation data. apical_tension The apical tension applied by the controller at sim_time. mpactsdata.csv Per-cell data extracted from simulation snapshots. Column Name Description cellName Name of the cell. time Simulation time. volumePressure The internal pressure of the cell. volume, area The cell's volume (um3) and surface area (um2). is_mitotic, is_dividing Boolean flags for the cell's state in the cell cycle. delta_centroids.csv Final positional deviation of simulated cells from their target positions. Column Name Description cell_name Name of the cell. centroid_x, _y, _z The final position of the cell centroid in the simulation. target_x, _y, _z The target position of the cell centroid from segmentation data. events.csv A log of all discrete events triggered during the simulation. Column Name Description type The type of event ('CellDivision' or 'ApicalTension'). cellName The cell associated with the event. start_time The simulation time when the event is triggered. direction_x, _y, _z The direction vector for cell division. spindleOffset The offset for asymmetric cell division.