mechanobiology

Unified Python/CLI time-series decomposition library with native acceleration, multivariate workflows, and machine-readable outputs.

A python package to analyze the matrix fiber orientation and intensity around cells in fiber matrices (as a proxy for cellular forces).

Python package to infer tensions from 2D microscopy images of embryos and tissues

Python research framework for finite-strain biomechanics, growth and remodeling, constituent turnover, and constrained-mixture modeling of soft tissues, with a verified NumPy–DOLFINx/MPI backend workflow

Finite Element Analysis to predict cranio-facial bone remodeling in response to tongue and jaw pressures over long periods of time.

Measure per-fiber mechanical tension in 3D ECMs from confocal line scans using Fiber Tension Microscopy (FTM).

A collection of manuals for the software tools used in mechanosensitive ion channel research, single-molecule imaging, and cell biology

Cephalic furrow project repository

Mechanogenomic virtual-cell model linking substrate stiffness, nuclear mechanotransduction, YAP/TAZ activity, and fibrosis-associated transcriptional trajectories.

A Python-based application for analyzing PIEZO1 protein distribution and membrane dynamics using TIRF microscopy data.

Interactive Polymer Network Mechanics & Free Body Diagram Simulator (Jacobs, Huang, & Kwon Fig 3.3)

Python code created for the Pathak lab to help analyze TIRF recordings of PIEZO1.

Automated 3D morphometric pipeline to quantify nuclear hypertrophy in Cdh2-deficient zebrafish embryos using Python and Streamlit.

Traceable reduced-order Python framework for multiscale knee mechanobiology, uncertainty propagation, validation maturity, reproducible benchmarks, and a research dashboard—explicitly not a clinical model.

GUI application for analyzing the relationship between cell-membrane curvature and PIEZO1 protein locations from fluorescence microscope recordings

Modular pipeline combining DECODE localization, MAGIK tracking, and ROI-based calcium analysis

Python pipeline for analyzing PIEZO1 protein localization and cell edge dynamics using fluorescence microscopy data.

GPU-native, fine-grained mechanistic simulator of single-cell mechanobiology — every filament, motor, adhesion, and cross-link is an explicit particle, not a lumped model. 177k LOC, validation-first, literature-anchored.

Bio-Resonant Restoration - Epigenetic Memory Reactivation via Piezoelectric Resonance: A Mechanistic Framework for Cellular Restoration

Mechanotransduction-resolved multiscale model of bone adaptation (MATLAB). Load enters as force; strain is a regulated output. Eight held-out observations recovered, including Frost's mechanostat set point emerging at 762 microstrain.