Glossary¶
- Model¶
In DendroTweaks, a computational representation of a neuron that includes its morphological structure, membrane properties, and simulation parameters necessary for numerical simulation.
- Tree graph¶
A hierarchical graph structure where nodes are connected by edges, with no cycles and a single path between any two nodes.
- Node¶
The fundamental unit of which graphs are formed.
- Edge¶
A connection between two nodes in a graph.
- Tree traversal¶
An algorithmic process of visiting each node in a tree graph exactly once.
- Reconstruction¶
A digital representation of a neuron’s three-dimensional morphology, composed of interconnected points with spatial coordinates.
- SWC file¶
A standard text-based file format for storing neuronal morphology data, where each line represents a point with its type, coordinates, radius, and parent point index.
- Point¶
A discrete location in 3D space representing a specific position in a neuronal reconstruction, defined by x, y, z coordinates and associated properties.
- Section¶
A continuous unbranched segment of a neuron between points of topological change (bifurcations).
- Domain¶
A collection of sections sharing common morphological or physiological characteristics, typically corresponding to parts of a neuron such as soma, dendrites, axon, etc.
- Segmentation¶
The process of dividing a section into smaller segments to discretize the spatial domain for numerical simulation.
- Segment¶
A small subunit of a section resulting from the segmentation process, used to approximate the spatial properties of a neuron.
- Segment Group¶
A collection of segments selected based on specific criteria such as domain, diameter, or distance.
- Membrane mechanism¶
A mathematical model describing the electrical properties of a neuronal membrane, such as ion channels and pumps.
- MOD file¶
A NEURON-specific file containing the implementation of membrane mechanisms, defining their mathematical equations and computational behavior.
- Parameter¶
A quantitative variable describing specific neuronal properties, such as membrane capacitance, ion channel conductance, or other physiological characteristics.
- Distribution¶
A mathematical function that assigns parameter values across neuronal structures based on spatial or morphological relationships.
- Synapse¶
A specialized junction enabling signal transmission between neurons, represented computationally as a point of conductance and kinetic changes.
- Population¶
In DendroTweaks, a group of “virtual” neurons that form synapses on the postsynaptic neuron (the model). The synapses in a population share the same kinetic and activation properties.