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.

Expand the list of available measurements and their definitions for outlines.

Area Type: Morphology, Per Time Point Area is the area encompassed by the object with sub-pixel accuracy. Area to Image Size Ratio Type: Morphology, Per Time Point Area to Image Size Ratio is the ratio of the Area of the object to the area of the entire image. Aspect Ratio Type: Morphology, Per Time Point Aspect Ratio is the ratio of the height of the object’s bounding box to the width of the object’s bounding box. Open Open Bounding Depth Type: Morphology, Per Time Point Bounding Depth is the extent in Z of the object’s bounding box.

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.

Spine

Spine measurements are separated into three (3) tabs in the Spreadsheet section of Aivia: the “Spines” tab for whole-spine measurements that include both the spine heads and necks, the “Spine Heads” tab for spine-head measurements, and the “Spine Necks” tab for spine-neck measurements. Spine heads and necks each inherit all mesh measurements. Additional spine measurements, which can be found in the “Spines” tab, are listed in the expandable panel below.

Whole cell

In Aivia, whole cells are composed of up to six (6) types of objects: cell membranes, nuclear membranes, cells, nuclei, cytoplasms, and vesicles. A cell and its cell membrane are represented by the same mesh (for 3D cells) or outline (for 2D cells); likewise, a nucleus and its nuclear membrane are represented by the same mesh/outline. The cytoplasm is not explicitly visually represented but is considered to be the volume or area in the cell that is not inside the nucleus, if one exists. Each vesicle is represented by its own mesh, spot, or outline.

The 3D Cell Analysis recipes establish relationships between 3D cellular components, and the Cell Analysis recipe establishes relationships between 2D cellular components. Each cell can have only one (1) nucleus, and each nucleus can be in only one (1) cell. Vesicles may fall outside of cells or can be in one (1) of four (4) categories: on a cell membrane, in a cytoplasm, on a nuclear membrane, or in a nucleus. Vesicles that are assigned to the cell membrane intersect the surface of the cell-membrane/cell mesh (for 3D cells) or edge of the cell-membrane/cell outline (for 2D cells), and vesicles that are assigned to the nuclear membrane intersect the surface of the nuclear-membrane/nucleus mesh (for 3D cells) or edge of the nuclear-membrane/nucleus outline (for 2D cells). Vesicles in the cytoplasm are inside of the cell and outside of the nucleus; they touch neither the surface/edge of the cell-membrane mesh/outline nor the surface/edge of the nuclear-membrane mesh/outline. Vesicles in the nucleus are inside of and do not touch the surface/edge of the nuclear-membrane mesh/outline.

Cell membrane

2D cell membranes inherit all outline measurements and can also have the measurements listed in the expandable panel below. A cell-membrane outline includes the entire area of what is considered the cell in Aivia.

3D cell membranes inherit all mesh measurements and can also have the measurements listed in the expandable panel below. A cell-membrane mesh includes the entire volume of what is considered the cell in Aivia.

Nuclear membrane

Nuclear membranes can have all the same measurements as cell membranes (see previous section).

Vesicle

Vesicle outlines inherit all outline measurements and can also have the measurements listed in the expandable panel below.

Vesicle meshes and spots can have all measurements listed in the expandable panel below. Vesicle meshes can additionally have all mesh measurements. Vesicle spots can have select mesh measurements: Bounding Depth, Bounding Height, Bounding Width, Centroid X, Centroid Y, Centroid Z, Max Intensity, Mean Intensity, Min Intensity, Std. Dev. Intensity, and Total Intensity.

Cell

Cytoplasm

In Aivia, the cytoplasm is the space inside of the cell membrane and outside of the nuclear membrane, if it exists.

Nucleus

In Aivia, the nucleus is the space inside of the nuclear membrane.

Relation

Relations between object sets can be defined using the Object Relation Tool in the Spreadsheet.

Track relation

References

1. Bresenham JE. (1965) Algorithm for computer control of a digital plotter. IBM Systems Journal. 4(1):25-30. doi: 10.1147/sj.41.0025

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