CorticalSW_Inference

Code to reproduce results from the paper:

Capone, Cristiano, et al. "Simulations Approaching Data: Cortical Slow Waves in Inferred Models of the Whole Hemisphere of Mouse." arXiv preprint arXiv:2104.07445 (2021).

Data used are available in the EBRAINS Knowledge Graph platform.

The paper articulates in the following steps:

• Inner Loop: inference parameters though maximum likelihood methd -> to execute this stage run the matlab codes 'InnerLoop.mat' and 'OuterLoop.mat' in the 'Inference' folder

• Data convolution -> (for simulated data) to execute this stage run the code within DataConvolution directory

• Cobrawap pipeline application -> to run thi stage follow instruction within the DataAnalysisWorkflow directory

  The analysis workflow used in this paper is a modified version of COBRAWAP tool described in this paper

• Data post-processing and visualization -> to execute this stage run codes in PostProcessing directory. To do so, analysis results should be organized as follows

  • Output: directory the output of the analysis. It should contain:
    • ConvolvedData: directory containing the convolved data from simulation. Each simulation output should be saved in a directory named "[mouse_number]_t[trial_number]_Ampl_Period"
    • The output of the Cobrawap pipeline on the experimental data saved in directories with name "TI_LENS_[mouse_number]_t[trial_number]"
    • The output of the Cobrawap pipeline on the simulated data grid search saved in directories with name "TI_MF_LENS_[mouse_number]t[trial_number][Almplitude_value]_[Period_value]"
    • The output of the Cobrawap pipeline on the simulated data from inner loop saved in directories with name "TI_MF_LENS_[mouse_number]_t[trial_number]_InnerLoop"

  The output figures will be saved in OutputPlot directory.