Measurement definitions

This page has definitions for measurements found in the General tab of the Measurements window. The Measurements window is accessed through the Measurement Tool icon in the Spreadsheet. The Object Classifier and some recipes automatically generate Advanced Measurements, and the equations for such measurements are shown in the Advanced tab of the Measurements window. Custom measurements can also be added, removed, and edited in the Advanced tab. Colocalization measurements can be added in the Colocal tab.

Outline

Outlines are 2D objects defined by closed sets of line segments.

Whole image outline

Whole image outlines may be composed of separate, closed 2D shapes on multiple image frames that are grouped as one object in Aivia. Whole image outlines are generated by the Wound Healing recipe.

Mesh

Meshes are 3D objects defined by closed sets of triangles.

Track

Track sets can either be made up of tracked outlines or tracked meshes; tracked outlines (2D tracks) can have all outline measurements in addition to track measurements, and tracked meshes (3D tracks) can have all mesh measurements in addition to track measurements. Tracks that have lineages (parent/child tracks) can also have lineage measurements.

Lineage

Lineage measurements are for tracks that have parents and/or children and are not calculated for tracks that are not part of lineages.

Neuron

Neurons are made up of up to four (4) basic components: somas, dendrite segments, spine heads, and spine necks.

Neuron

Neuron measurements are available for neuron objects with somas.

Soma

Somas inherit all mesh measurements except Centroid X, Centroid Y, Centroid Z, Bounding Depth, Bounding Height, and Bounding Width. Somas can also have Dendrite Count, which is the same as the neuron measurement of the same name, and Neuron ID, which is the number of the neuron object to which the soma is associated.

Dendrite

Dendrites inherit all mesh measurements and have a few additional measurements, which are listed in the expandable panel below. Dendrite measurements are available for whole dendrites trees in the Dendrite Trees tab of the Spreadsheet and for individual dendrite segments in the Dendrite Segments tab of the Spreadsheet. Dendrite segments are composed of sets of dendrite points (nodes), which are defined in 3D space by their location and diameter.