Spindle Orientation Model

A simulation of mitotic spindle orientation inside a cell cortex, driven by astral microtubules (pushing) and cortical force-generator motors (pulling). Supports three cell/organism systems: fly follicular epithelium/neuroblast, C. elegans (pronuclei centering and metaphase/anaphase spindle positioning), and zebrafish embryonic cells (using real tracked-movie cell shapes).

Contents

• spindle_model.py — the model (single file, no build step).
• Spindle_Simulator.ipynb — widget-driven notebook for running a single simulation interactively (works locally or on Google Colab).
• data/ — tracked-movie inputs for the zebrafish cell type (cell shapes, spindle masks, junction coordinates, movie metadata).

Requirements

Python 3 with numpy, matplotlib, opencv-python, pandas, openpyxl, shapely, scipy, and ipywidgets (only needed for the notebook UI).

Quickstart (notebook)

Open Spindle_Simulator.ipynb and run the cells top to bottom — pick a cell type, adjust the settings, click Run simulation.

Quickstart (Python)

from spindle_model import run_simulation

results = run_simulation(
    cell_type="FE",       # "FE" | "celegans" | "endo"
    motor_density=10,     # motor count (FE/celegans) or density (endo)
    n_astral_mt=50,
    push=1, pull=0,
    spindle_length=0.8,   # model units; FE and celegans "spindle" mode only
    total_time=600,       # seconds; None -> cell-type default
)

Key kwargs: neuroblast=True (FE apical-only placement), celegans_mode="PNC"|"spindle", endo_cell_number=<n> (required for cell_type="endo"; see list_available_endo_cells()), initial_angle, time_step, seed, advanced={...} (override physical constants). Returns a dict of result arrays (angle, position, push/pull counts vs. time) and writes an .xlsx to data_folder_path.

Quickstart (command line / Slurm)

python spindle_model.py <test_folder_path> <data_folder_path> <run_name>

run_name encodes the cell type (via a cell_<Type> token) and every parameter as regex tokens, e.g.:

spindle_9214_cell_FE_MUD_10_MT_50_push_1_pull_0_ts_0.05_AL_1_state_default_angle_45_SL_1.8

MUD=motor density, MT=astral MT count, push/pull=on-off flags, ts=time step, AL=astral MT length distribution, state=MT state-init mode, angle=initial spindle angle, SL=spindle length. For celegans runs, the name must also contain _PNC_ or _position_; for zebrafish/endo runs, a cell_<n> token selects the tracked cell. Reads SLURM_ARRAY_TASK_ID/SLURM_JOB_ID if set, otherwise runs as a plain local command.

Cell types

• FE — fly follicular epithelium / neuroblast (idealized elliptical cell).
• celegans — C. elegans embryo; PNC (pronuclei centering) or spindle (metaphase/anaphase positioning) sub-modes.
• endo — zebrafish embryonic cell, using a real cell shape tracked from a movie (requires the matching entry under data/).

Units: lengths are in model units (1 model unit = 10 µm); time is in seconds.