ITK library to sample events into regular volumes
High-level description of the main applications currently supported by Fivox.
Real scientific use cases, coming from user requests and finished after a collaboration with scientists:
Compute the LFP signal at the extracellular space of a given circuit, based on a simulation current report (more info).
The output is generated as a 3D volume, containing each of the voxels the LFP value corresponding to the position at the center of the voxel.
For completeness, a separate tool (sample-point) is provided, to generate the time series of the output voltage at a specific 3D point. In this case the space is not voxelized, and the computation is done for a single point, so the resulting values are more accurate, as an exact 3D position is used as input (as opposed to the voxelized space, in which several different points within a same voxel take the same value). The output is a text file with one value per timestep, being possible to plot this values in order to visualize the evolution of the voltage over time as a 2D graph.
Generate the in-silico VSD optical imaging of a given circuit, based on the compartment areas and simulation voltage report (more info).
A separate tool is provided, with the ability to generate a 2D image with the floating point values, representing the projection on the pial surface of the brain; and also a 3D volume containing the VSD values for each of the compartments (before the projection step).
Generate a 3D volume with the synapse distributions, with the count of synapses per voxel, for the given pre and post-synaptic targets.
Solutions that could be (or already are) implemented, but without a clear application, as they don't fulfill any real scientific need:
Generate a 3D volume with the spike frequencies per voxel, for the given circuit and spike report.
Generate a 3D volume representing the influence of the compartment voltages in the extracellular space (e.g. applying a square falloff) for a given circuit.