File format used to store large amounts of scientific data. HDF5

cross section

A cross section of a cell process at a point is the intersection of that cell process with the plane perpendicular to the tangent of its longitudinal axis at that point. The actual shape of this intersection is not known, so it has to be simplified (see also point and perimeter).


In a cell process, the perimeter at a point is the perimeter of its cross section. This is specially necessary for astrocytes because the circular approximation for the cross sections can differ greatly from the real perimeter and does not suffice for geometrical modelling.


A point with no children. By definition, it has to be the last point in a section.


Either an ‘axon’, ‘basal dendrite’, or an ‘apical dendrite’ type of section.


A 4-vector composed of floating point numbers. The first three columns represent X, Y, and Z coordinates and the last column represents the diameter. Units: micrometers.


A series of points bounded by any viable combination of branching point (BP), root-point (RP), and end-points (EP). That is, any of

  • RP-BP

  • BP-BP

  • BP-EP

  • RP-EP.

A branching point is the boundary between a section and one or more child sections.

The first point of a section duplicates the last point of its parent, unless the parent is a the soma.


The shortest representable portion of a neurite. A segment is constituted by 2 consecutive points belonging to the same neurite section.


The central cell body of a neuron.

glia endfoot

A glia process that makes contact with a blood vessel.

postsynaptic density

It’s a standard neuroscience term. On the postsynaptic side in electron microscope images, a blob of dark material that appears to be very dense is seen.