Basic parameter: Parameter used by the LNeuron program to create virtual cells. Directly measured and encoded in LNeuron algorithm.

Bif_amp_local: LMeasure function which returns the angle in degrees between the first two compartments.

Bif_amp_remote: LMeasure function which returns the angle in degrees between a bifurcation point and the end of the two branches it leads to (next terminal tip or bifurcation).

Bif_tilt_local: LMeasure function which returns the angle in degrees between a father compartment (last compartment before a bifurcation) and its daughter compartments (first two compartments following a bifurcation. Smaller of two possible values returned.

Bif_tilt_remote: LMeasure function which returns the angle in degrees between a father compartment and its two daughter branches (next terminal tip or bifurcation). Smaller of two possible values returned.

Bif_torque_local: LMeasure function which returns the angle between the plane of a bifurcation (defined by the end points of the first two compartments following a bifurcation) and the plane of the previous bifurcation (defined the same way).

Bif_torque_remote: LMeasure function which returns the angle between the plane of a bifurcation (defined by the point of bifurcation and the end of it’s two daughter branches, either the next bifurcation or terminal point) and the plane of the previous bifurcation (defined the same way).

Branch_pathlength: The LMeasure function which returns the path length of a branch, that is the distance from bifurcation to the next bifurcation or termination. Also see termlength and conslength.

Cvapp: Program which allows viewing and editing of SWC files.

Daughter_Ratio: LMeasure function which returns the ratio of the diameters of the first segments of the two daughters following a bifurcation. It is defined as the diameter of the larger daughter / diameter of the smaller daughter. Also the LNeuron parameter which controls the ratio of the daughter diameters following a bifurcation.

Dendro1: Software program which takes a digitized neuron in swc format outputs a separate file for each tree off of the neuron containing a dendrogram representation of that tree in swc format.

Dendrogram: Two dimensional representation of the branching pattern of a neuron where length, diameter and branching are conserved while all angle information is ignored.

Diameter: LMeasure function which returns the diameter of a compartment. Used with the specificity N_stems=1 to extract diameter information on the beginning of a tree (see initdiam).

Diam_threshold: LMeasure function which returns the diameters of the two compartments half way between a bifurcation leading to directly to two terminal tips and those tips themselves. Also the LNeuron parameter which controls the diameter value below which a dendritic process will not bifurcate.

Emergent parameter: Parameter which is not directly encoded in the LNeuron algorithm. Used as a check to determine if the algorithm is accurately and completely representing the real neurons.

Ibf_Branch_pathlength: LNeuron parameter which controls the length of interbifurcation branches. Measured using LMeasure function Branch_pathlength with a specificity of N_tips >= 1.

Length: LMeasure function which returns the length of a compartment. Sum line is used to get total length of a dendritic process.

Lmeasure: Software package which extracts many shape parameters from digitized neurons.

LNeuron: Software program which uses statistical distributions measured from real cells to create virtual cells.

N_bifs: LMeasure function which returns 1 if compartment is a bifurcation point (leads directly to two daughter compartments). Sum of bifurcations used as an emergent parameter.

N_stems: LMeasure function which returns one if compartment is a stem (connected to the soma). Also LNeuron parameter which controls how many trees of a given type are on each generated neuron.

N_tips: LMeasure function which returns the number of terminal tips a compartment leads to. Used as a specificity to separate terminal from interbifurcation branches (will be one for terminal tips, greater than one for all interbifurcation branches).

PK (Poliko): The LMeasure function which returns the value which creates the best fit in the Ralls formula (PK*dpralls=d1ralls+d2ralls) where dp, d1, and d2 are the diameters of the parent and two daughters respectively. The Lmeasure functions Poliko_15 ( called Poliko_classic in older LMeasure versions) and Poliko_2 return this value for each bifurcation assuming a Ralls exponent of 1.5 and 2 respectively. The Poliko function returns this value using the Ralls value computed for each bifurcation. Also The LNeuron parameter which adjusts the Ralls formula according to (PK*dpralls=d1ralls+d2ralls) where dp, d1, and d2 are the diameters of the parent and two daughters respectively.

Rall_Power: LMeasure function which returns the exponent in the Ralls formula (dpralls=d1ralls+d2ralls) where dp, d1, and d2 are the diameters of the parent and two daughters respectively. The two classic values are 2 (conserves volume), and 1.5 (conserves surface area). Also the LNeuron parameter which controls the Ralls power exponent used to generate the diameter of the first daughter based on the diameter of the parent compartment.

Stem_Diameter: LNeuron parameter which controls the starting diameter of a generated dendritic tree. Measured using LMeasure diameter function with a specificity of N_stems = 1.

Taper_2: LMeasure function which returns the length independent percent of decrease in diameter. Defined as initial diameter end diameter / initial diameter. Also the LNeuron parameter which controls the change in diameter as a dendritic process is generated.

Term_Branch_pathlength: Length of a segment from the last bifurcation in a branch to the terminal tip. Measured using the LMeasure function Branch_pahtlength with the specificity of N_tips=1.

Volume: LMeasure function which returns the volume enclosed by a compartment. The sum line of this returned data is used to get the volume occupied by and entire dendritic process. Used as an emergent parameter.