EFMouse: 1 x 1 with craniotomy montage
EFMouse is a Matlab tool for electric field modelling in the mouse brain.
This notebook reproduces results for the 1 x 1 with craniotomy montage in:
Sanchez-Romero R., Akyuz, S., & Krekelberg, B. (2025). EFMouse: a toolbox to model electric fields in the mouse brain. bioRxiv. https://doi.org/10.1101/2024.07.25.605227
The notebook is also an introductory tutorial to simulate other montages.
(Developed by Ruben Sanchez-Romero and Bart Krekelberg,
Rutgers-Newark, Center for Molecular and Behavioral Neuroscience,
for support open an issue in https://github.com/klabhub/EFMouse/issues)
Table of Contents
Introduction
EFMouse combines several elements from previous work:
- Anatomical data from the Digimouse project.
- A refined finite element mesh of the Digimouse by Alekseichuk et al., (2019), Neuroimage.
- Matlab code and inspiration from the ROAST toolbox.
- The GetDP finite element method (FEM) solver (v 3.5.0).
- The Allen mouse brain atlas.
Key new functionality includes:
- Positioning electrodes in arbitrary locations in and on the mouse body.
- Modeling craniotomies in the mouse skull.
- Analyzing the electric field in user-defined regions of interest
- Analyzing the electric field in brain regions defined in the Allen mouse atlas.
- A measure of relative focality of the electric field.
- A measure of direction homogeneity of the electric field.
For details see Sanchez-Romero et al., (2025) and EFMouse.m Matlab code.
Typical workflow
The typical workflow to generate a model consists of several stages
- Stage.INIT : Initialize.
- Stage.MESH : Define elecrodes and (optionally) a craniotomy.
- Stage.EXPORT : Export files for the FEM solver GetDP.
- Stage.GETDP : Run the FEM solver.
- Stage.ATLAS : Map the results to the Allen mouse atlas.
Stage INIT: Initialize
We start by setting up the basic parameters of the EFMouse object:
o = EFMouse; % Create a default empty object of the class EFMouse
o.ID = '1x1_craniotomy'; % A name/tag for this simulation.
o.dir = '/Users/rubensanchez/desktop/efmouse_sim/1x1_craniotomy'; % Results and the object (1x1_craniotomy.mat) will be saved here.
o.log = true; % Create a log file.
Note: The log file is created but doesn't update when running a simulation from a notebook (like here). It will properly update when running EFMouse directly from the Matlab command line.
initialize() creates the folder to store the results. With overwrite=true, anything in this folder will be deleted.
o.initialize(overwrite=true);
The initialized EFMouse object contains the default mouse mesh (without stimulation electrodes). Let's visualize the brain tissue. You can select different tissues to visualize.
plotMesh(o,tissue='gray')
The mesh is pretty dense, so it may look like a black blob. The olfactory bulbs are visible on the top. In a regular figure window, you can use the Matlab figure tools to rotate or zoom. (You can also adapt the plotMesh() function in EFMouse.m to modifiy the figure directly.)
Stage MESH: Create electrodes and a craniotomy
Now we define a 1x1 stimulation montage, targeting visual areas. The surface type is an electrode that is placed on top of the animal (simulating how gel would be placed on the skin).
o.addElectrode(tag = "Anode",current = 0.2,type="surface",shape="circle",center= [-3.5,30,6],radius=0.6, thickness=1);
o.addElectrode(tag = "Cathode",current = -0.2,type="surface",shape="circle",center= [-3.5,25,6],radius=0.6, thickness=1);
Add a craniotomy between the stimulation electrodes. Select the material replacing the space where skin and bone were removed. Here, we simulate a dry craniotomy where only air flows into the space left by the removed skin and bone.
o.addCraniotomy(tag = "left",center=[-3.5,27.5,6],radius=1.5,material=["air","air"]);
To update the model with the electrodes and the craniotomy, we run the pipeline to Stage.MESH. With show=true, this also opens a figure for inspection of the mesh:
o.run(targetStage=Stage.MESH,show=true)
This mesh shows the electrodes in red (anode) and blue (cathode). For the craniotomy, the two tissue types that have been removed (skin and bone) are shown in cyan and magenta.
Stage EXPORT: export the mesh and model
Up until this stage, all changes were internal to the Matlab object (saved in 1x1_craniotomy.mat), now we export files that the FEM solver GetDP can read. The .msh file contains information on the mesh (all the nodes, elements, labels and boundaries), and the .pro file tells GetDP which partial differential equations (PDE) model it needs to solve in this mesh.
o.run(targetStage=Stage.EXPORT)
For troubleshooting, have a look at the .pro file in the project folder; it contains all the model specifications, including conductivity (in siemens per meter S/m) for the different tissues/elements.
type(file(o,"PRO"))
This file can be opened in the GetDP gui to run it manually, but Stage.GETDP runs it for you.
Stage GETDP: run GetDP
It will take GetDP between 15 and 30 minutes to compute the solutions of the Laplace equation (on 2024 Mac or Windows hardware). The results are saved in _e.pos and _v.pos files (in GetDP format). In the object the results are saved as .field and .voltage.
o.run(targetStage=Stage.GETDP,show=false);
Use the plotEf() function to visualize the electric field in the X direction, and then the electric field magnitude.
plotEf(o,type='eX',percentile=98, tissue='gray');
plotEf(o,type='eMag',percentile=98,tissue='gray');
We can also use plotEf() to visualize a brain slice perpendicular to a given axis. Here we show a frontal/coronal plane slice (perpendicular to the y axis) in the position of the anode electrode, a sagittal slice and a horizontal slice.
plotEf(o,type='eMag',percentile=98,tissue='gray',slice = true, slice_ax = "y",slice_pos = 27)
plotEf(o,type='eMag',percentile=98,tissue='gray',slice = true, slice_ax = "x",slice_pos = -2)
plotEf(o,type='eMag',percentile=98,tissue='gray',slice = true, slice_ax = "z",slice_pos = 3.5)
Tissue Based Analysis
In general, we focus on the brain, but if necessary, we can compute electric field estimates for the rest of the mouse body for a full characterization of the anatomical effects of the electrical stimulation protocol. leftbone refers to the bone area removed during the craniotomy. The label is defined by joining the craniotomy tag (see Stage MESH above) and the tissue removed: left + "bone": leftbone.
See Sanchez-Romero et al., (2025) for a full description of the electric field metrics.
summary = analyzeTissue(o,["skin" "gray" "leftbone"]);
ROI Analysis
Now that we have the field estimates for each node in the mesh, we can do an ROI based analysis. For instance, a box ROI.
For the relative focality the reference area is the rest of the gray tissue.
See Sanchez-Romero et al.(2025), for definitions of relative focality and homogeneity.
roi.shape = 'box';
roi.center = [-3.5,27.5 3.5];
roi.width = 2; % Left/Right
roi.length = 2; % Anterior/Posterior
roi.thickness =1; % Inferior/Superior
summary = analyzeRoi(o,roi,plot=true,foc_percentile_max=99.9,foc_threshold=40); % Define values for relative focality metric.
% Rotate and zoom to view the (yellow) box ROI underneath the craniotomy
xlim([-3.31 1.13])
ylim([26.3 36.1])
zlim([2.31 4.98])
view([62.61 27.62])
For comparison, define an analogous box ROI but in the right hemisphere
roiRight = roi;
roiRight.center(1) =-1* roi.center(1)
summary = analyzeRoi(o,roiRight,plot=true,foc_percentile_max=99.9,foc_threshold=40);
% Rotate and zoom to view the (yellow) box ROI in the right hemisphere
xlim([-3.31 1.13])
ylim([26.3 36.1])
zlim([2.31 4.98])
view([62.61 27.62])
Stage ATLAS: Volumetric/Atlas Analysis
The mesh coordinates are not particularly intuitive, and you may want to estimate electric fields in specific brain areas (as defined in an atlas). EFMouse does this in reference to the Allen Mouse Brain Atlas.
To use this, we first have to map the mesh-based results to the Allen Atlas. This is Stage ATLAS of the pipeline. This stage first exports the mesh-based results to a volume (using linear interpolation) and then uses the FLIRT tool in FSL to transform this volume to the coordinates of the Allen Atlas. Note that the alignment between the Digimouse mesh and the Allen Atlas is not perfect because they are based on different imaging modalities (and different mouse strains). (See Sanchez-Romero et al., (2025), for more details.)
This will fail if FSL is not installed.
o.run(targetStage=Stage.ATLAS,startStage=Stage.ATLAS)
Atlas Based Analysis
Once stage 5 has completed we can query electric fields based on a region that is defined in the Allen Atlas. For instance: 'Visual areas' for the left hemisphere.
For the relative focality the reference area is the rest of the Allen atlas "Isocortex".
T = analyzeAtlas(o,"Visual areas",hemisphere="left",foc_threshold=40,foc_percentile_max=99.9,foc_reference='Isocortex');
For comparison, we can query results for the right hemisphere, which is contra-lateral from the targeted area.
T = analyzeAtlas(o,"Visual areas",hemisphere="right",foc_threshold=40,foc_percentile_max=99.9,foc_reference='Isocortex');
Tips and Tricks
- The run function can be called with any targetStage from Stage.INIT to Stage.ATLAS. Stages that have already been completed will not be run again, and all stages that need to be completed to reach the targetStage will be completed in turn.
- IMPORTANT: To continue working with a model from a previous Matlab session, you create an EFMouse object with the dir and ID input arguments to specify the folder with the (previously saved) results and the ID of the montage. For instance, to open the simulation from the tutorial at the stage where it was last saved:
o = EFMouse(dir='/Users/rubensanchez/desktop/efmouse_sim/1x1_craniotomy',ID='1x1_craniotomy')