DOI: 10.5061/dryad.612jm64k7
title: Chemotaxis-driven Instabilities govern size, shape and migration efficiency of multicellular clusters

description: This dataset documents experimental and simulation-based measurements of
 collective chemotactic migration and dynamical behavior of multicellular
 cell clusters. It includes processed experimental data derived from
 time-lapse microscopy of chronic lymphocytic leukemia (CLL) cell clusters
 exposed to controlled gradients of the chemokine CCL19 (0–100 ng ml⁻¹
 mm⁻¹). Image-based measurements were extracted using Fiji/ImageJ and
 include cluster size, centroid trajectories, migration velocities, shape
 descriptors, and orientation of the cluster’s major axis relative to the
 chemical gradient, reported in pixel units. The dataset also contains
 processed outputs from particle-based and agent-based simulations spanning
 multiple cluster sizes and gradient strengths. Simulation variables
 include forward migration index, mixing entropy, spatial and orientational
 correlations, shape metrics, rotational dynamics, and cluster breaking
 frequencies. Scripts used to compute quantitative metrics and reproduce
 summary analyses are provided. Together, these data support quantitative
 analyses of collective chemotactic responses, shape deformation, and
 instability-driven dynamics in multicellular systems and provide reusable
 benchmarks for studies of collective migration and active matter.
description: # Chemotaxis-driven Instabilities govern size, shape and migration
 efficiency of multicellular clusters Dataset DOI:
 [10.5061/dryad.612jm64k7](https://doi.org/10.5061/dryad.612jm64k7) ##
 Description of the data and file structure This dataset accompanies the
 article *“Chemotaxis-driven instabilities govern size, shape and migration
 efficiency of multicellular clusters”* and contains experimental and
 simulation data quantifying collective chemotactic migration, shape
 deformation, orientation, and breakup of multicellular clusters.
 Experimental data were obtained from time-lapse microscopy of chronic
 lymphocytic leukemia (CLL) cell clusters exposed to controlled CCL19
 gradients (0–100 ng ml⁻¹ mm⁻¹). Processed measurements extracted using
 Fiji/ImageJ include cluster size, centroid position, shape metrics, and
 the orientation of the major axis relative to the chemical gradient,
 reported in pixel units. Simulation data consist of processed outputs from
 agent-based models spanning multiple cluster sizes and gradient strengths,
 including forward migration index, entropy, correlations, shape metrics,
 rotation, and breaking frequencies. Together, these data enable analysis
 of chemotaxis-driven instabilities and provide reusable benchmarks for
 studies of collective migration and cluster dynamics. The dataset contains
 no personal or identifiable information and has no ethical or legal
 restrictions beyond citation of the associated publication. ### Files and
 variables #### File: DataForPaper.zip **Description:**  ## **Folder
 Structure** The deposited dataset contains two main folders: ### **1.
 ExperimentalData/** Processed measurements extracted from time-lapse
 microscopy of CLL cell clusters migrating under CCL19 gradients. These
 experimental data are used to calculate the orientation of the cluster’s
 major axis relative to the direction of the chemical gradient, as a
 function of cluster size. Contents: *
 **AngleAspect_Orientation_of_Cluster/expt.csv** Processed breaking
 probability for a representative experiment. *
 **G0-100Angle/combined_angles.csv** Combined angle data aggregated across
 eight experiments (9Apr2014, 14Feb2014, 17Oct2013, 22Dec2014, 23Oct2013
 Nikon Gradient Slopes, 26Nov2013 Nikon, Position4_9Dec2013). *
 **Subfolders for individual experiments**, each containing processed CSV
 along with the actual experimental file: * 9April2014/ * 14Feb2014/ *
 17Oct2013/ * 22dec2014/ * 23ct2013NIKON Gradient Slopes/ * 26nov2013NIKON/
 * Position4_9Dec2013/ Each folder may contain the following files: *
 \***.tif** — original image file * \***(0–100).tif** — cropped
 experimental region (0–100), if available * *Results*(0–100).csv* —
 measurement results for the cropped region, if generated The CSV file
 contains measurements exported from Fiji/ImageJ (Analyze → Measure) for
 segmented intensity clusters. **Units** * Lengths & positions: pixels
 (px) * Area: square pixels (px²) * Intensity: raw grayscale values
 (arbitrary units) **Columns** * Area (px²): Cluster size * Mean / Min /
 Max: Pixel intensity statistics * XM, YM (px): Cluster centroid
 coordinates * Major / Minor (px): Ellipse major & minor axes * Angle
 (deg): Orientation of major axis (from x-axis) * Circ.: Circularity (1 =
 perfect circle) * Slice: Image slice index * AR: Aspect ratio
 (Major/Minor) * Round: Roundness (based on major axis) * Solidity:
 Area/convex area (1 = solid) ### **2. SimulationsData/** Processed summary
 outputs extracted from simulations of cluster migration under varying
 gradients and cluster sizes. #### Files include: *
 **averaged_data_angle_with_cluster_fraction_size.csv** *
 **BreakingFrequency_size-grad_gdep_250.txt** *
 **ClusterQuantification_size-grad_gdep_250.txt** *
 **Entropy_con-gradHeatmap.txt** *
 **entropy_contours_all_levels_plus_extra.csv** *
 **entropy_contours_all_levels.csv** * **entropy_contours_thresholds.csv**
 * **Entropy_size-gradHeatmap.txt** * **FMI_con-grad_gdep_37_Heatmap.txt**
 * **FMI_size-grad_gdep_250_Heatmap.txt** *
 **full_data_angle_with_cluster_fraction_size.csv** *
 **ROTation_size_grad_gdep_250.txt** * **ROTationdata.txt** These represent
 the processed results used to generate the figures in the paper, including
 FMI, entropy, correlations, shape metrics, and breaking frequencies. ####
 **A. TimeSeriesData/XXX/RUN_0001/ to RUN_0010/**
 TimeSeriesData/N_XX_pcore_XX_noff_XX_grad_X.XXXX_gdep_250/RUN_0001/ to
 RUN_0010/ In the folder name: * **N_XX**: size of the cluster *
 **pcore_XX**: active propulsion strength of the core particles *
 **noff_XX**: noise offset * **grad_X.XXXX**: chemical gradient strength *
 **gdep_250**: concentration at the center of mass (CM) of the cluster
 ##### **Each RUN_XXXX folder contains:** #### **data/** Reduced simulation
 frames or processed particle positions. * **Ovito.xyz** Main data file
 containing time-resolved particle information (load using the OVITO
 application). Columns: ParticleTypeID, ClusterID, x, y, r, vx, vy, nx, ny,
 gx, gy * **velocityvst.txt** Time-resolved center-of-mass data: time,
 x_cm, y_cm, v_x, v_y #### **analysis/** Summary outputs including cluster
 size, velocities, shape evolution, breaking probability, and orientation
 over time. * **CMFrame.xyz** Ovito.xyz with particle positions shifted to
 the cluster center-of-mass (CM) frame. * **ZeroToBoxLx.xyz** Ovito.xyz
 shifted to a 0 → L box reference (from −L/2 → L/2). *
 **colorCodedOvito.xyz** Ovito.xyz with particles color-coded by cluster
 ID. * **CM_with_layers.xyz** Cluster in the CM frame, color-coded into
 three layers, used to calculate mixing entropy. *
 **clusterNumber_vs_time.txt** Number of clusters and particles per cluster
 at each frame. * **entropy_time_data.txt** Mixing entropy as a function of
 time. * **clusterRotationData.txt** Cluster dynamical properties (rotation
 and motion) as a function of time. * **output.txt** Time-resolved shape
 metrics of the cluster: time, major_axis_length, minor_axis_length,
 angle_with_x * **ROG.txt** Radius of gyration and shape tensor–based
 quantities: t, xx, xy, yy, radiusOfGyration, asymmetry, compactness,
 principal_dir_x, principal_dir_y ### **Data Variables** **Experimental
 Data Variables** * **Angle** – Cluster orientation relative to the +x
 cdirection (degrees). * **Frame / Time** – Time index of the movie
 (frames). * **x, y** – Cluster centroid position (pixels or µm). *
 **Size** – Cluster size or projected area (cell count or pixels). All
 files include column names as descriptions that explain the variables
 contained in each dataset. **Simulation Data Variables** * **FMI** –
 Forward migration index (dimensionless). * **Entropy** – Mixing entropy of
 cluster layers (dimensionless). * **AspectRatio** – Ratio of major/minor
 cluster axes. * **BreakFrequency** – Number of breaking events. *
 **CorrelationCrossing** – Distance where velocity correlation crosses zero
 (cell diameters). * **Gradient (g_r)** – Chemical gradient strength (model
 units). * **Velocity** – Cell or cluster speed (model units). *
 **Position_x, Position_y** – Position coordinates (model units). **Missing
 Values** Missing values are indicated as **blank cells** or **NaN**. No
 special placeholders are used. **Files and Data Notes** Raw simulation
 trajectories and raw video files are not deposited due to size limits, but
 are available upon request. ## Code/software 1. **Experimental videos**
 were opened in **Fiji**, where clusters were segmented, and measurements
 (angle, size, position) were extracted. 2. **Simulation trajectories**
 (*.xyz files) were visualized in **OVITO** . 3. **Processed CSV/TXT
 files** were analyzed in **Python**, where all quantitative analysis and
 plotting were performed using the provided scripts.