How to measure cell values

  • Important for measuring of morphological paprameters of cells generated by NeuGen:
  • Parameters which can be accessed via the GUI output:
    • For each single cell:
      • total length of dendrites
      • total length of axon
      • total surface area of dendrites
      • total surface area of axon
      • soma location
      • number of primary dendrites
      • total number of dendritic segments
      • total number of axonal segments
      • number of axonal branches
    • For all cells:
      • total number of synapses
      • total number of non-functional synapses
      • In the generated file 'average_neuron_info.csv'(csv= comma separated values) you can find the following information e.g.: cell_type; number of dendrites; total_denlength; deviation; total_axlength; deviation; total_densurface_area; deviation; total_axsurface_area; deviation; number_axnparts; deviation; total_dennparts; deviation; number_axbranches; deviation; L5Apyramidal;7;7546.77;504.087;7610.76;2988.59;14058.2; 622.14;6003.63; 2295.53;1381.1;361.5;1604.4;107.68;25.5;7.2

        These values represented the network, i.e., they are generated by all cells.
      • The description of the identifiers is as follows:
        • number of dendrites
        • total_denlength: total dendritic length
        • total_axlenth: total axonal length
        • total_densurface_area: total dendritic surface area
        • total_axsurface_area: total axonal surface area
        • number_axnparts: number of axonal compartments in the model
        • total_dennparts: number of dendritic compartments in the model
        • number_axbranches: total number of axonal branches
        And the subsequent 'deviation' value gives always the SD-value of the corresponding parameter.

        Moreover, as many configuration parameters are set by the corresponding mean values of the morphological parameter, these parameters can be taken as the mean values since the NeuGen algorithm uses them to sample from distribution with an ensemble mean given by these values.