The zip file has the program to generate trees. There are 243 variants that varies based on which parameters control which aspects of dendritic growth. lnded2_0.class is the main file. It takes two comand line parameters, an input file (the .prn parameter file) and an output file name. Program reads the parameter file, reads and processes the swc files listed in the parameter file, and generates new swc files. Detailed Instruction: Nanda S, Das R, Bhattacharjee S, Cox DN, Ascoli GA (2018) Morphological determinants of dendritic arborization neurons in Drosophila larva. Brain Struct Funct 223(3):1107–1120. This models is a slight adaptation from the Donohue and Ascoli (2008) paper. Model descriptions and directions. Overview: The model is for creating virtual branching structures based on 3D reconstructions of real neurons. The model takes as input a parameter file (FileList.prn) which gives the file path of several neuronal reconstructions in .swc format. Five basic parameters are measured from each branch of the input neurons; branching probability, taper rate, daughter ratio, parent daughter ratio, and branch length. They are then organized and reduced to statistical distributions based on three fundamental determinants (FDs); radius, path distance from the soma, and branch order. The distributions are then placed into a table file. Morphometrics are resampled from the tables based on the current virtual fundamental determinant values to create virtual 2D branching structures. Each basic parameter can be controlled by a separate FD. Given that there are 5 basic parameters and 3 FDs, there are 5^3, or 243 unique variants of this model. Note that the three cases where all five parameters are under the control of the same FD are equivalent to the three percent mix cases where one FD has 100% influence (although due to differences in random number generation they are only statistically identical and will not provide the exact same results). In either case these are referred to as "pure" models. Running the program: The models are designed to be executed from the command line. The format (in mswin) is: Java lnded2_0 inputFileName OutputFilePostfix Where lnded2_0 is the .class file created from the .java files included in each directory. The input file is a text file with the extension of .prn in our examples. See the ExampleCommandLine.bat file for a specific example. When the program is run a table file prefixed "Table_" is created which gives the statistical distributions of the basic parameters binned by FDs. For each bin a distribution type (Uniform (1), Gaussian (2), and Gamma (3)) is chosen based on a least mean squares matching between the real data and generated data of each distribution type. An empty file is "OutputInfo_ " file is also created. If the "DEBUGGING" switch is set to "true" in the .prn file (explained below) this "OutputInfo_" file will be filled with all of the raw data used to create the table file. Finally, four .csv files are created beginning with "VirtAsymetry_", "VirtBifs_", "VirtSurface_", and "VirtSurfaceAsym_". These contain the group means and standard deviations for bifurcation asymmetry, bifurcation numbers, surface area, and surface area asymmetry of the virtual trees for each model variant. The mean and standard deviation of the given emergent morphometric for the real input trees is included at the end of the file. .prn file options: The following are the options which can be adjusted through the parameter file. For each option the value to be assigned is placed on the following line of the .prm file. Unless otherwise noted all options apply to both model variants. INPUT Takes an integer value referring to the number of .swc files which are to be loaded. On subsequent individual lines the full file path of each input files is given. A large number of .swc files are available at NeuroMorpho.org. TODO Takes an integer value giving the number of group of virtual trees to create. If for example there were 12 input .swc files with three trees each and TODO is set to 10 (the default value) then 10 groups of 36 virtual trees will be created. The mean and standardizations given in the .csv files refer to theses group means and standardizations. BINNING Takes an integer value giving the minimum number of points to be placed into each FD bin. The default is 85. It is important to note that this is the minimum and for those FDs which can be heavily discretized (branch order and radius) bins may contain many more data points than this. For example, if there are 50 input branches of branch order 1, 75 of branch order 2, and 130 of branch order three the first bin will contain 125 data points and the second 130 if the minimum is set at 85. TYPETODO Takes an integer which specifies which tree type to be analyzed and recreated from the .swc file. The default is 3 (regular or basal dendrite). 4 (apical dendrite) and 2 (axon) are also accepted as is any custom type value. MINRAD Takes a positive double value specifying the minimum allowed radius. Because the model is stochastic it is possible to continue reducing the radius values of virtual trees beyond realistic boundaries. This value specifies the radius values below which termination is not allowed. Default is .15. SEED Takes an integer and sets the random number seed value. Useful for doing multiple runs without getting the exact same results each time. DEBUGGING Takes either "true" or "false". Boolean which if true (default) populates the file prefixed with "OutputInfo_" with many details about the input .swc files parameter values. SWCOUT Takes either "true" or "false". Boolean which if true writes a separate .swc file for each virtual tree created for analysis by external programs. Because no 2D or 3D information is included these files will appear as single lines in visualization software. Default is false. DENDRO Takes either "true" or "false". Boolean which if true writes a separate .swc file for each virtual tree created in the form of a 2D dendrogram. These files are useful for visualization and figures, but the lateral offset which separates the branches adds length to the trees which is not part of the model. Default is false. PERCENTSTEP not needed for this version of the model. Default in 0.1.