Getting Started with Electrophysiology (MFHN model)

Description

• This example will guide you through the creation of a new electrophysiology model using a Modified Fitzhugh-Nagumo model (Rogers & McCulloch, 1994, IEEE Transactions on Biomedical Engineering, 41:743-757) to explore a reentrant wave case.

• The files required are located in the examples directory on your Continuity client .../continuity/pcty/examples/electrophysiology20/

• The steps below are saved in a script that can be found in [here MFHN_2D_script.py] and can be executed automatically with File→Read→Python script

Start Continuity

• Launch the Continuity 6.3 Client

• On the About Continuity 6.3 startup screen

  • check the Electrophysiology module box under Use Modules:

Create Mesh

• Mesh→Edit→Coordinates…

  • Select rectangular cartesian in the Global Coordinates: pop-up menu

  • Click OK to submit Coordinate Form

• Mesh→Edit→Basis…

  • Choose Hermite Basis Function→2D→Cubic-Cubic with 2 integration/collocation points for Xi 1 and Xi 2

  • Click Add

  • Choose Lagrange Basis Function→2D→Linear-Linear with 2 integration/collocation points for Xi 1 and Xi 2

  • Click Add

  • Click OK to submit Basis Form

• Mesh→Edit→Nodes…

  • Click Import/Export/Graph button to open Continuity Table Manager

    • Continuity Table Manager→File→Open…

      • Select tab-delimited nodes file attachment:nodes_CrashingWaves.txt

      • Continuity Table Manager→File→Close and update form

  • Select Linear-Linear Lagrange 2*2 under Coordinate 1, Coordinate 2, Coordinate 3, Fiber angle, Sheet angle, and Transverse angle

  • In the Field Vector 1 tab, select Linear-Linear Lagrange 2*2 under Field Variable 1 and Field Variable 3

  • In the Field Vector 2 tab, select Cubic-Cubic Hermite 2*2 under Field Variable 2

  • Click OK to submit Node Form

• Mesh→Edit→Elements…

  • Click Import/Export/Graph button to open Continuity Table Manager

    • Continuity Table Manager→File→Open…

  • Select tab-delimited elements file attachment:elems_CrashingWaves.txt

    • Continuity Table Manager→File→Close and update form

  • Click OK to submit Element Form

• Mesh→Edit→Material Coordinates…

  • Select MatCoordStandard:Standard Material Coordinates

    • Verify the source of your fiber angle orientation. Same field location as the one indicated in the Nodes form, or using a fixed fiber angle.

      • Submit the Material Coordinates Form

• Otherwise, upload the Cont6 file located at the Continuity folder, File→Load→Model…

  • Find the Cont6 file: pcty/examples/electrophysiology20/2D_mfhn_REENTRY_Crashing_waves.cont6 and load it

• Calculate mesh from Mesh→Calculate Mesh and click OK

Formulate Electrophysiology Problem

• If the Electrophysiology menu is not loaded, File→Load Module

  • Select Electrophysiology and click Load Module

• Electrophysiology→Edit Ionic Model…

  • Select the EP_MFHN_reentry_sympy model

  • Locate the ‘Submit’ tab and click Submit

• Initialize the EP model by clicking on Electrophysiology→Solve→Initialize…

• Calculate the no-flux Boundary Conditions of the model in Electrophysiology→Calculate→Constraints…

  • Choose the default Fix out-of-plane boundary node derivatives and click OK

  • Send all data to the server

• Go to the Render elements icon and render the surface

  • Make sure you are using the OpenMesh renderer at View→Change Renderer→Open Mesh…

  • Click OK

• Your model is ready to Solve

Compute and Render Solutions

• Electrophysiolgoy→Solve→Integration…

  • Choose a ‘File name’ distinction

  • Input 900 ms as the duration for the simulation

  • Go to the Output tab and input a display solution interval of 20 steps

  • Go back to the Integrate tab and click on OK

• When your simulation has finished, you can render the solutions by Electrophysiology→Render→Render Solution…

  • Set Min Value to 0

  • Set Max value: to 1

  • Click OK to view an animated color map of the Action Potential propagation

Electrophysiology Example in the BiVentricular Dog Anatomy (MFHN)

• Select Cont6 file attachment:mfhn_dog_48.cont6

• You can follow the previous steps, or run the file with the following script: attachment:mfhn_dog_48script.py

• Now you can experiment by changing various characteristics:

  • location of the stimulus (modifying Field Variable 1)

  • the Diffusion coefficient from Isotropic to Anisotropic
  • the fiber angle

  • refining the mesh and adding transmural fiber heterogeneity attachment:mfhn_dog_fib.cont6

* Happy Modelling!