EMSIM

EMSim is a library that computes different electro-magnetic effects like LPF and VSD.

Features

EMSim provides the following functionality:

In order to compute LFP or VSD, there are a few common initial steps:

1. Load the circuit data from a circuit file
2. Create all the static morphology geometry
3. Apply current and voltage report on the geometry
4. Finally, specific calculations are done to compute LFP or VSD

The LFP part of EMSim computes the electric field in the space between neurons, using the following method:

1. Load and place all segments in 3D space
2. Load the current report for each segment and for every simulation frame
3. Create a volume with the specified resolution (# of voxels)
4. Compute the value for each voxel, using the current point model (one can also compute the values of some sample points instead of the full volume)

The VSD part of EMSim simulates the processes of a voltage sensitive dye, using the following method:

1. Load and place all segments in 3D space
2. Load the voltage report for each segment and for every simulation frame
3. Create a volume with the specified resolution (# of voxels)
4. For each voxel, the value is accumulated
5. Create a projection of the volume into a 2D surface

Installation

With a proper installation of Brion, installation can be done with CMake:

$ mkdir build $ cd build $ cmake .. -GNinja $ ninja

See the CI plan for more details.

Usage

emsim

The emsim program has the following options:

-i [ --input ] arg Path to Blueconfig file. -o [ --output ] arg Path for the output file. --target arg The circuit's target. --report arg The name of the report. --start-time arg The start time --end-time arg The end time --fraction arg Specify the fraction [0.0 1.0] of gids to be used during the computation. Default is 1.0. --export-volume Will export a floating point volume for each time steps. --voxel-size arg The size in each dimension of a voxel in circuit units. Default is 4.0,4.0,4.0. Must be written in the form: --voxel-size rx,ry,rz --volume-extent arg Specify an additional 3d extent for the volume in micrometers. Default is 0.0,0.0,0.0. Must be written in the form: --volume-extent ex,ey,ez --sample-point arg The x y z positions of a sample point. Must be written in the form: --sample-point x,y,z

So, for example, to compute the LFP values on 2 probes: emsim \ -i blueconfigFile \ -o outputFileName \ --target cuirtcuitTarget \ --report currentReport \ --sample-point 12,34,32 \ --sample-point 43,56,43 \

emsimVSD

The emsim program has the following options:

-i [ --input ] arg Path to Blueconfig file. -o [ --output ] arg Name of the output volume (if 'export-volume' specified) and 2D image files --target arg The circuit's target. --report-voltage arg The name of the voltage report in the BlueConfig. --report-area arg The name of the area report in the BlueConfig. --sensor-res arg (=512) Number of pixels per side of the square sensor. --sensor-dim arg (=1000) Length of side of the square sensor in micrometers. --curve arg Path to the dye curve file (default: no attenuation) --start-time arg The start time of the simulation --end-time arg The end time of the simulation --time-step arg The time between frames, in milliseconds --fraction arg Specify the fraction [0.0 1.0] of gids to be used during the computation. Default is 1.0. --export-volume Will export a floating point volume for each time steps. --depth arg (=2081.7561) Depth of the attenuation curve area of influence. It also defines the Y-coordinate at which it starts being applied down until y=0 (default: 2081.756 micrometers). --interpolate-attenuation Will interpolate the attenuation curve. --sigma arg (=0.00449999981) Absorption + scattering coefficient (units per micrometer) in the Beer-Lambert law. Must be a positive value (default: 0.0045). --v0 arg (=-65) Resting potential (default: -65 mV). --g0 arg (=0) Multiplier for surface area in background fluorescence term. --ap-threshold arg (=3.40282347e+38) Action potential threshold in millivolts. --soma-pixels Produce a text file containing the GIDs loaded and their corresponding 3D positions and indices in the resulting 2D image.

For example, to compute the VSD with 1000um sensor size with a 512 resolution:

emsimVSD \ -i blueconfigFile \ -o outputFileName \ --target cuirtcuitTarget \ --report-voltage voltageReport \ --report-area areaReport \ --sensor-dim 1000 \ --sensor-res 512

Input Formats

VSD Curve File

When using the --curve option, a file must be supplied. This is a depth-dependent dye attenuation curve file that contains a column of floating point values, one for every micrometer specified by the --depth argument

Output Format

LFP

export-volume

Triggered by the export-volume option.

sample-point

This writes a file called $output$_sample_points where $output$ is the value of the --output argument. Lines in this file starting with # are comments; For each frame in the report a line is generated with the following format:

timestamp samplePoint1 samplePoint2 ... samplePointN

Where the samplePointN is the voltage at that point.

export-volume

Triggered by the export-volume option.

This option writes two files (where $output$ is the value of the --output argument): * a raw file called: $output$_volume_floats$timestamp$.raw for each frame, containing the LFP voxel values for each voxel * a txt file called $output$_volume_info_$timestamp$.txt for each frame.

VSD

• $output$_image_floats_$timestamp$.raw, containing the raw binary data of the 2 dimensional viewport.
• an MHD file for each frame called $output$_image_floats_$timestamp$.mhd, containg the header information for the above.

volume-info

This option writes two files (where $output$ is the value of the --output argument): * $output$_volume_floats_$timestamp$.raw, much like the one from LFP. * an MHD file for each frame called $output$_volume_floats_$timestamp$.mhd, containing the header imformation for the above.

Acknowledgement & Funding

This project was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government's ETH Board of the Swiss Federal Institutes of Technology.

Copyright (c) 2017-2024 Blue Brain Project/EPFL