Spheroid-Trap-Designer

The MMFT spheroid-trap designer is a tool that generates a microfluidic chip and/or channel design for trapping spheroids based on hydrodynamic principles in a dedicated location on a chip, by employing a SAT solver to optimize the design process and automatically compute the required parameters while adhering to ISO guidelines. It is possible to chain several traps together and thereby trap several spheroids. These traps are especially useful for studying complex biological processes such as the vascularization of spheroids and organoids [1].

The tool is available online: https://www.cda.cit.tum.de/mmft-spheroid-trap-desiger. It is part of the Munich Microfluidics Toolkit (MMFT) by the Chair for Design Automation at the Technical University of Munich.

If you have any questions about the fabrication and the trapping experiments feel free to contact us at microfab@cea.fr. If you have questions about using or the development of the code write us via microfluidics.cda@xcit.tum.de or by creating an issue on GitHub.

System Requirements

The project is tested with python 3.11. To install the required python packages please type the following in your command line:

    pip install -r requirements.txt

Run

To run the script, via the command line, type:

    python spheroid_all.py

You can adapt the parameters in the same script.

Simulation Setup

The Spheroid Trap Designer allows you to generate a customized geometry based on your specified parameters. Once the geometry is created, you can simulate fluid flow within it. For this you can use OpenFOAM, an open-source computational fluid dynamics (CFD) tool, COMSOL, a commercial CFD tool, or any other tool. For OpenFOAM and COMSOL we have included some of the simulation files that can be adapted for personal use.

OpenFOAM

Before proceeding, ensure that OpenFOAM is installed on your system. Installation instructions can be found on the official OpenFOAM website. The set up described here is tailored for OpenFOAM 12.

Simulation Setup Guide

1. Generate the Geometry

• Define your parameters and generate the spheroid trap geometry via the web interface or by running the provided command-line tool.
• The generated STL file will represent the 3D shape of the trap. The generated STL is defined in mm, here the STL is automatically scaled to size.

2. Prepare for Simulation

• Copy the generated STL file into the following directory: (You might need to generate the geometry folder)

  /simulation/openFoam/constant/geometry

• Rename the STL file to trap.stl.
• Modify the vertices in the blockMeshDict file to ensure the mesh properly fits around your geometry:

  /simulation/openFoam/system/blockMeshDict

  Important: The block mesh needs to "cut-off" the inlet and the outlet so these can be defined as specialized boundaries, i.e., that an inflow or outflow can be defined. Currently the block mesh is defined for a trap input for spheroids with a diameter of 300 µm.

3. Run the Fluid Flow Simulation

• Navigate to the OpenFOAM simulation directory:

  cd /simulation/openFoam

• Start the simulation by executing:

  run

This will generate the computational mesh and simulate fluid flow within your custom spheroid trap.

COMSOL

The comsol simulation files are uploaded in the simulation folder. You can change the simulation paremeters via COMSOL's GUI.

Stationary model

Run the stationary study to simulate the fluid flow.

Transient model

First run the stationary study to initialize and then the transient study to simulate the spheroid's trajectory.

References

[1] Quintard, C., Tubbs, E., Jonsson, G. et al. A microfluidic platform integrating functional vascularized organoids-on-chip. Nat Commun 15, 1452 (2024).

Developed in collaboration between: