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<..> Necessary parameter. If any parameter is missing the function will run in interactive mode.
[..] key stroke
(...) data type (int, float, string)

It converts ".pa" files <input_file> generated by Micro3D visualization software to ASCII files <output_file>. Moreover, it extracts blocks of data from the ".pa" files that defined by structure_name. In order to generate layer id-s the user must provide the coordinate for the starting layer <start_layer> and layer increment <step_layer>. These numbers must be defined based on the original data. Based on these, the function generate integer layer ID numbers corresponding to different z-coordinates of the cells.

It generate a selection of cell coordinates proportional to the local density. The selection is based on random sampling the cells in a unit spaces. First the function calculates the density of cells (or any 1 dimensional markers) from the data presented as input_file with multiple columns where n_columns determines the number of columns and control_string determines the coordinates of the 3D database (1=xyz coordinates, 2 section ID). For example the control string 11102 means that the x,y and z coordinates are contained by the first second third columns and the section ID is represented by the fifth column. The output_file is a 3D array where each layer is encoded by a block of ASCII float data. Width_of_cube and length_of _cubetogether with the section thickness define the voxel, a volume within which the density of cells is calculated. Since sections of different markers can be non-continuous N_section defines the number os sections, start_section is the first section to calculate and section_widthis the width of sections from the input file. This value is needed for generating a Neurolucida data file output. The mult_factor is a constant multiplicative factor that scales the logarythm of the number of cells per voxels. The resulting number of cells will be selected from a given voxel. The selection is a random choice of the cells from the voxel. If the mult_factor is 1 the log of the local cellcount is used.

See also cubdensrnd-threshold.

Same as cubdensrnd but instead of selecting cells based on the scaled logarithm of voxel density it select the number of cells simply based on a threshold defined by the threshold parameter.

See also cubdens-vol.

It calculates the density of cells (or any 1 dimensional markers) from the data presented as input_file with multiple columns where n_columns determines the number of columns and control_string determines the coordinates of the 3D database (1=xyz coordinates, 2 section ID). For example the control string 11102 means that the x,y and z coordinates are contained by the first second third columns and the section ID is represented by the fifth column. The output_file is a 3D array where each layer is encoded by a block of ASCII float data. Width_of_cube and length_of _cubetogether with the section thickness define the voxel, a volume within which the density of cells is calculated. Since sections of different markers can be non-continuous N_section defines the number os sections, start_section is the first section to calculate and step_section is the step size between successive sections.
See also cubdens-vol-absref.

Same as cubdens-vol except it calculates the density within a volume defined by x_min, x_max, y_min and y_max coordinates. Moreover, this metrics provides a reference frame to compare and combine densitograms from different tracing data or accross different individuals.
See also cubdens-vol.

Function for constructing the density ratios between two databases given as input_file1 and input_file2. The output_file contains the volumetric array of the ratio between input_file2 and input_file1 as ratio=input_file2/input_file1. The output is organized in ASCII blocks where each block is a 2D layer in the volumetric data. The control_string determines the coordinates of the 3D database (1=xyz coordinates, 2 section ID). For example the control string 11102 means that the x,y and z coordinates are contained by the first second third columns and the section ID is represented by the fifth column.  For the density calculation the database is first limited to a volume defined by x_min, x_max, y_min and y_max. This volume then will be subdivided into small blocks of width_of_cube and length_of _cube voxels. Within each voxel the ratio of the two markers is calculated and written to the output_file.  Since the input database may not obtained from a continuous volume you have to define the number of sections (n_section) the starting sections (start_section1 and start_section2) and the section gap (offset) between successive sections.   You can also limit the space of density calculation to voxels of minimal density by min_dens.

Same as cubdens-comp-vol except it generates an output with the markers extracted from the original database that represents volumes where the density ratio is smaller or equal as the one given by crit_dens. The extracted markers are appended to an ASCII output that is dumped to the actual output terminal or file (using > filename). This output contains  a neurolucida data file that can be imported by using the Mto the actual output terminal or file (using > filename). This output contains  a neurolucida data file that can be imported by using the Microbrighfield's Neurolucida or Neuroexplorer system. In practice this output can be appended to a preexisting Neurolucida database providing structure outlines and cell markers. Colorstr is a colorstring for the marker color.
See also cubdens-comp-vol.