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.

Type: Morphology, Per Time Point

Area is the area encompassed by the object with sub-pixel accuracy.

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.

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.

Type: Morphology, Per Time Point

Bounding Depth is the extent in Z of the object’s bounding box.

Type: Morphology, Per Time Point

Bounding Height is the extent in Y of the object’s bounding box.

Type: Morphology, Per Time Point

Bounding Width is the extent in X of the object’s bounding box.

Type: Morphology, Per Time Point

Breadth is the length of the minor axis of a best-fit ellipse for the object.

Type: Position, Per Time Point

Center of Mass X is the x-coordinate of the object’s Center of Mass. The Center of Mass is calculated as the average (mean) of the positions of all vertices of the outline.

Type: Position, Per Time Point

Center of Mass Y is the y-coordinate of the object’s Center of Mass. The Center of Mass is calculated as the average (mean) of the positions of all vertices of the outline.

Type: Position, Per Time Point

Centroid X is the x-coordinate of the center of the object’s bounding box.

Type: Position, Per Time Point

Centroid Y is the y-coordinate of the center of the object’s bounding box.

Type: Position, Per Time Point

Centroid Z is the z-coordinate of the center of the object’s bounding box.

Type: Morphology, Per Time Point

Circularity is a measure of how circular an object is and is defined by the equation below. The circularity of a circle is one (1).

Type: Intensity, Per Time Point

Coefficient of Variation is the ratio of the standard deviation of the intensity of a given channel in the pixel-based area encompassed by the object to the mean intensity of the same channel and area. Outlines are pixelated using a custom algorithm that is derived from Bresenham’s line algorithm [1] as well as a filling algorithm. The image channel for the measurement is indicated in the measurement name; for example, the Coefficient of Variation for a channel named “GFP” is called “Coefficient of Variation (GFP)” or “Coefficient of Variation - GFP.”

Type: Count, Per Time Point

Component Count is the number of related objects within the object.

Type: Morphology, Per Time Point

Length is the length of the major axis of a best-fit ellipse for the object.

Type: Morphology, Per Time Point

Length/Breadth Ratio is the ratio of the length of the major axis to the length of the minor axis of a best-fit ellipse for the object.

Type: Intensity, Per Time Point

Mean Intensity is the mean intensity of a given channel in the area encompassed by the object. Sub-pixel estimation is used to calculate Mean Intensity. The image channel for the measurement is indicated in the measurement name; for example, the Mean Intensity for a channel named “GFP” is called “Mean Intensity (GFP)” or “Mean Intensity - GFP.”

Type: Morphology, Per Time Point

Object Angle is the angle between the major axis of an ellipse that is fit to the object and the x-axis. In the example below, the Object Angle is dθ.

Type: Morphology, Per Time Point

Perimeter is the sum of the lengths of all line segments that make up the outline of the object.

Type: Morphology, Per Time Point

Pixel-based Area is the area of the object with pixel-level accuracy. Outlines are pixelated using a custom algorithm that is derived from Bresenham’s line algorithm [1] as well as a filling algorithm.

Type: Intensity, Per Time Point

Pixel-based Max Intensity is the maximum intensity of a given channel in the area encompassed by the object without sub-pixel estimation. Outlines are pixelated using a custom algorithm that is derived from Bresenham’s line algorithm [1] as well as a filling algorithm. The image channel for the measurement is indicated in the measurement name; for example, the Pixel-based Max Intensity for a channel named “GFP” is called “Pixel-based Max Intensity (GFP)” or “Pixel-based Max Intensity - GFP.”

Type: Intensity, Per Time Point

Pixel-based Mean Intensity is the mean intensity of a given channel in the area encompassed by the object without sub-pixel estimation. Outlines are pixelated using a custom algorithm that is derived from Bresenham’s line algorithm [1] as well as a filling algorithm. The image channel for the measurement is indicated in the measurement name; for example, the Pixel-based Mean Intensity for a channel named “GFP” is called “Pixel-based Mean Intensity (GFP)” or “Pixel-based Mean Intensity - GFP.”

Type: Intensity, Per Time Point

Pixel-based Median Intensity is the median intensity of a given channel in the area encompassed by the object without sub-pixel estimation. Outlines are pixelated using a custom algorithm that is derived from Bresenham’s line algorithm [1] as well as a filling algorithm. The image channel for the measurement is indicated in the measurement name; for example, the Pixel-based Median Intensity for a channel named “GFP” is called “Pixel-based Median Intensity (GFP)” or “Pixel-based Median Intensity - GFP.”

Type: Intensity, Per Time Point

Pixel-based Min Intensity is the minimum intensity of a given channel in the area encompassed by the the object without sub-pixel estimation. Outlines are pixelated using a custom algorithm that is derived from Bresenham’s line algorithm [1] as well as a filling algorithm. The image channel for the measurement is indicated in the measurement name; for example, the Pixel-based Min Intensity for a channel named “GFP” is called “Pixel-based Min Intensity (GFP)” or “Pixel-based Min Intensity - GFP.”

Type: Intensity, Per Time Point

The Pixel-based Standard Deviation Intensity is the standard deviation of the intensity of a given channel in the area encompassed by the object without sub-pixel estimation. Outlines are pixelated using a custom algorithm that is derived from Bresenham’s line algorithm [1] as well as a filling algorithm. The image channel for the measurement is indicated in the measurement name; for example, the Pixel-based Standard Deviation Intensity for a channel named “GFP” is called “Pixel-based Standard Deviation Intensity (GFP)” or “Pixel-based Standard Deviation Intensity - GFP.”

Type: Intensity, Per Time Point

The Pixel-based Total Intensity is the sum of all intensities for a given channel in the area encompassed by the object without sub-pixel estimation. Outlines are pixelated using a custom algorithm that is derived from Bresenham’s line algorithm [1] as well as a filling algorithm. The image channel for the measurement is indicated in the measurement name; for example, the Pixel-based Total Intensity for a channel named “GFP” is called “Pixel-based Total Intensity (GFP)” or “Pixel-based Total Intensity - GFP.”

Type: Intensity, Per Time Point

Total Intensity is the sum of all intensities for a given channel in the area encompassed by the object with sub-pixel estimation. Sub-pixel estimation is done using a sample of intensities along the outer edge of the outline with the equations below, where nv is the number of vertices the outline has along its outer edge, I(x, y) is the intensity of the pixel at the uncalibrated location (x, y), and (xi, yi) is the uncalibrated location of vertex i. The image channel for the measurement is indicated in the measurement name; for example, the Total Intensity for a channel named “GFP” is called “Total Intensity (GFP)” or “Total Intensity - GFP.”

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.

Type: Morphology, Per Time Point

Bounding Depth is the extent in Z of the object’s bounding box.

Type: Morphology, Per Time Point

Bounding Height is the extent in Y of the object’s bounding box.

Type: Morphology, Per Time Point

Bounding Width is the extent in X of the object’s bounding box.

Type: Position, Per Time Point

Centroid X is the x-coordinate of the center of the object’s bounding box.

Type: Position, Per Time Point

Centroid Y is the y-coordinate of the center of the object’s bounding box.

Type: Position, Per Time Point

Centroid Z is the z-coordinate of the center of the object’s bounding box.

Type: Intensity, Per Time Point

Outline Whole Image Mean Intensity is the mean intensity of a given channel in the area encompassed by all outlines making up the object on the current frame with sub-pixel accuracy. The image channel for the measurement is indicated in the measurement name; for example, the Outline Whole Image Mean Intensity for a channel named “GFP” is called “Outline Whole Image Mean Intensity (GFP)” or “Outline Whole Image Mean Intensity - GFP.”

Type: Morphology, Per Time Point

Pixel-based Whole Image Area is the sum of the areas of all outlines making up the object on the current frame with pixel-level accuracy. Outlines are pixelated using a custom algorithm that is derived from Bresenham’s line algorithm [1] as well as a filling algorithm.

Type: Intensity, Per Time Point

Pixel-based Whole Image Max Intensity is the maximum intensity of a given channel in the area encompassed by all outlines making up the object on the current frame with pixel-level accuracy. Outlines are pixelated using a custom algorithm that is derived from Bresenham’s line algorithm [1] as well as a filling algorithm. The image channel for the measurement is indicated in the measurement name; for example, the Pixel-based Whole Image Max Intensity for a channel named “GFP” is called “Pixel-based Whole Image Max Intensity (GFP)” or “Pixel-based Whole Image Max Intensity - GFP.”

Type: Intensity, Per Time Point

Pixel-based Whole Image Mean Intensity is the mean intensity of a given channel in the area encompassed by all outlines making up the object on the current frame with pixel-level accuracy. Outlines are pixelated using a custom algorithm that is derived from Bresenham’s line algorithm [1] as well as a filling algorithm. The image channel for the measurement is indicated in the measurement name; for example, the Pixel-based Whole Image Mean Intensity for a channel named “GFP” is called “Pixel-based Whole Image Mean Intensity (GFP)” or “Pixel-based Whole Image Mean Intensity - GFP.”

Type: Intensity, Per Time Point

Pixel-based Whole Image Median Intensity is the median intensity of a given channel in the area encompassed by all outlines making up the object on the current frame with pixel-level accuracy. Outlines are pixelated using a custom algorithm that is derived from Bresenham’s line algorithm [1] as well as a filling algorithm. The image channel for the measurement is indicated in the measurement name; for example, the Pixel-based Whole Image Median Intensity for a channel named “GFP” is called “Pixel-based Whole Image Median Intensity (GFP)” or “Pixel-based Whole Image Median Intensity - GFP.”

Type: Intensity, Per Time Point

Pixel-based Whole Image Min Intensity is the minimum intensity of a given channel in the area encompassed by all outlines making up the object on the current frame with pixel-level accuracy. Outlines are pixelated using a custom algorithm that is derived from Bresenham’s line algorithm [1] as well as a filling algorithm. The image channel for the measurement is indicated in the measurement name; for example, the Pixel-based Whole Image Min Intensity for a channel named “GFP” is called “Pixel-based Whole Image Min Intensity (GFP)” or “Pixel-based Whole Image Min Intensity - GFP.”

Type: Intensity, Per Time Point

Pixel-based Whole Image Standard Deviation Intensity is the standard deviation of the intensity of a given channel in the area encompassed by all outlines making up the object on the current frame with pixel-level accuracy. Outlines are pixelated using a custom algorithm that is derived from Bresenham’s line algorithm [1] as well as a filling algorithm. The image channel for the measurement is indicated in the measurement name; for example, the Pixel-based Whole Image Standard Deviation Intensity for a channel named “GFP” is called “Pixel-based Whole Image Standard Deviation Intensity (GFP)” or “Pixel-based Whole Image Standard Deviation Intensity - GFP.”

Type: Intensity, Per Time Point

Pixel-based Whole Image Total Intensity is the total intensity of a given channel in the area encompassed by all outlines making up the object on the current frame with pixel-level accuracy. Outlines are pixelated using a custom algorithm that is derived from Bresenham’s line algorithm [1] as well as a filling algorithm. The image channel for the measurement is indicated in the measurement name; for example, the Pixel-based Whole Image Total Intensity for a channel named “GFP” is called “Pixel-based Whole Image Total Intensity (GFP)” or “Pixel-based Whole Image Total Intensity - GFP.”

Type: Position, Per Time Point

Whole Image Area is the area encompassed by all outlines making up the object on the current frame with sub-pixel accuracy.

Type: Position, Per Time Point

Whole Image Area to Image Size Ratio is the ratio of the Whole Image Area to the total area of the image frame.

Type: Morphology, Per Time Point

Whole Image Aspect Ratio is the ratio of the Bounding Height of the object to the Bounding Width of the object.

Type: Morphology, Per Time Point

Whole Image Breadth is the length of the minor axis of a best-fit ellipse for the object.

Type: Morphology, Per Time Point

Whole Image Circularity is a measure of how circular the object is and is defined by the equation below. The circularity of a circle is one (1).

Type: Intensity, Per Time Point

Whole Image Coefficient of Variation is the ratio of the standard deviation of the intensity of a given channel in the pixel-based area encompassed by all outlines making up the object on the current frame to the mean intensity of the same channel and area. Outlines are pixelated using a custom algorithm that is derived from Bresenham’s line algorithm [1] as well as a filling algorithm. The image channel for the measurement is indicated in the measurement name; for example, the Whole Image Coefficient of Variation for a channel named “GFP” is called “Whole Image Coefficient of Variation (GFP)” or “Whole Image Coefficient of Variation - GFP.”

Type: Count, Per Time Point

Whole Image Component Count is the number of related objects within the object.

Type: Morphology, Per Time Point

Whole Image Length is the length of the major axis of a best-fit ellipse for the object.

Type: Morphology, Per Time Point

Whole Image Length/Breadth Ratio is the ratio of the length of the major axis to the length of the minor axis of a best-fit ellipse for the object.

Type: Morphology, Per Time Point

Whole Image Perimeter is the sum of the perimeters of all outlines making up the object on the current frame.

Type: Intensity, Per Time Point

Whole Image Total Intensity is the total intensity of a given channel in the area encompassed by all outlines making up the object on the current frame with sub-pixel accuracy. The image channel for the measurement is indicated in the measurement name; for example, the Whole Image Total Intensity for a channel named “GFP” is called “Whole Image Total Intensity (GFP)” or “Whole Image Total Intensity - GFP.”

Type: Morphology, Per Time Point

Wound Closure Speed is the rate at which the percentage of the image area that is not covered by the object is changing based on the areas covered on the current and previous frames according to the equation below, where Δt is the time between frames.

Mesh

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

Type: Morphology, Per Time Point

Average Angle is the mean angle between the x-axis and all center line segments in radians.

Type: Morphology, Per Time Point

Average Length is the mean Euclidean distance between a vertex of the center line and the starting point of the center line for the mesh.

Type: Morphology, Per Time Point

Bounding Depth is the depth (extent in Z) of the object’s bounding box.

Type: Morphology, Per Time Point

Bounding Height is the height (extent in Y) of the object’s bounding box.

Type: Morphology, Per Time Point

Bounding Width is the width (extent in X) of the object’s bounding box.

Type: Morphology, Per Time Point

Center Line Length is the length of the skeletonized version of the mesh.

Type: Position, Per Time Point

Center of Mass X is the x-coordinate of the mesh’s Center of Mass. The Center of Mass is calculated as the average (mean) of the positions of all voxels contained by the mesh. If the mesh does not contain any voxels, meaning it does not cover more than 50% of a voxel, the Center of Mass is considered equal to the Centroid.

Type: Position, Per Time Point

Center of Mass Y is the y-coordinate of the mesh’s Center of Mass. The Center of Mass is calculated as the average (mean) of the positions of all voxels contained by the mesh. If the mesh does not contain any voxels, meaning it does not cover more than 50% of a voxel, the Center of Mass is considered equal to the Centroid.

Type: Position, Per Time Point

Center of Mass Z is the z-coordinate of the mesh’s Center of Mass. The Center of Mass is calculated as the average (mean) of the positions of all voxels contained by the mesh. If the mesh does not contain any voxels, meaning it does not cover more than 50% of a voxel, the Center of Mass is considered equal to the Centroid.

Type: Position, Per Time Point

Centroid X is the x-coordinate of the center of the object’s bounding box.

Type: Position, Per Time Point

Centroid Y is the y-coordinate of the center of the object’s bounding box.

Type: Position, Per Time Point

Centroid Z is the z-coordinate of the center of the object’s bounding box.

Type: Morphology, Per Time Point

CV of Lengths is the cumulative variance of the distances from each vertex of the mesh to the starting point of the mesh’s center line.

Type: Morphology, Per Time Point

Ellipsoid Longest Axis Length is the length of the longest axis of a best-fit ellipsoid for the mesh.

Type: Morphology, Per Time Point

Ellipsoid Second Longest Axis Length is the length of the second longest axis of a best-fit ellipsoid for the mesh.

Type: Morphology, Per Time Point

Ellipsoid Shortest Axis Length is the length of the shortest axis of a best-fit ellipsoid for the mesh.

Type: Morphology, Per Time Point

Equivalent Spherical Diameter is the diameter of a sphere that is fit to the mesh.

Type: Intensity, Per Time Point

Max Intensity is the maximum intensity for a given channel over all voxels that are completely contained by the mesh. This measurement is empty for meshes that do not contain any full voxels. The image channel for the measurement is indicated in the measurement name; for example, the Max Intensity for a channel named “GFP” is called “Max Intensity (GFP)” or “Max Intensity - GFP.”

Type: Intensity, Per Time Point

Mean Intensity is the mean intensity of a given channel over all voxels that are completely contained by the mesh. This measurement is empty for meshes that do not contain any full voxels. The image channel for the measurement is indicated in the measurement name; for example, the Mean Intensity for a channel named “GFP” is called “Mean Intensity (GFP)” or “Mean Intensity - GFP.”

Type: Intensity, Per Time Point

Min Intensity is the minimum intensity for a given channel over all voxels that are completely contained by the mesh. This measurement is empty for meshes that do not contain any full voxels. The image channel for the measurement is indicated in the measurement name; for example, the Min Intensity for a channel named “GFP” is called “Min Intensity (GFP)” or “Min Intensity - GFP.”

Type: Morphology, Per Time Point

Sphericity is a measure of how round the mesh is based on the relationship between the Surface Area and Volume and is calculated using the equation below.

Type: Intensity, Per Time Point

Std. Dev. Intensity is the standard deviation of the intensity for a given channel over all voxels that are completely contained by the mesh. This measurement is empty for meshes that do not contain any full voxels. The image channel for the measurement is indicated in the measurement name; for example, the Std. Dev. Intensity for a channel named “GFP” is called “Std. Dev. Intensity (GFP)” or “Std. Dev. Intensity - GFP.”

Type: Morphology, Per Time Point

Straight Center Line Length is the Euclidean distance between the endpoints of the center line of the mesh.

Type: Morphology, Per Time Point

Surface Area is the area of the object’s surface, which is the sum of the areas of all triangles making up the surface of the mesh.

Type: Morphology, Per Time Point

Surface Area to Volume Ratio is the ratio of the Surface Area to the Volume of the mesh.

Type: Morphology, Per Time Point

Top 5 Percent Length is the mean Euclidean distance from a vertex of the mesh to the starting point of the center-line for mesh vertices with Euclidean distances to the starting point that are in the top 5% for all vertices of the mesh.

Type: Intensity, Per Time Point

Total Intensity is the sum of the intensities for a given channel over all voxels that are completely contained by the mesh. This measurement is empty for meshes that do not contain any full voxels. The image channel for the measurement is indicated in the measurement name; for example, the Total Intensity for a channel named “GFP” is called “Total Intensity (GFP)” or “Total Intensity - GFP.”

Type: Morphology, Per Time Point

Volume is the volume of the mesh.

Type: Morphology, Per Time Point

Volume to Image Volume Ratio is the ratio of the Volume of the mesh to the total volume of the image.

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.

Type: Morphology, Per Time Point

Acceleration Angle is the planar angle between the acceleration vector and the x-axis in degrees. The acceleration vector for the object is estimated using the object’s current position, position at the two (2) previous time points, and the time between frames (Δt). This measurement is empty on the first two (2) time points of a track.

Type: Position, Per Time Point

Acceleration Magnitude is the magnitude of the acceleration vector for the object, which is estimated using the object’s current position, position at the two (2) previous time points, and the time between frames (Δt) with the equations below. This measurement is empty on the first two (2) time points of a track but uses the position of the parent track(s) if there were any lineage splits between the current frame and two (2) frames prior.

Type: Morphology, Per Time Point

The Curvature of a track at a certain time point is the reciprocal of the radius of the best-fit circle/sphere at that time point. In Aivia, Curvature (Κ) is calculated using the equation below, where dθ is the change in the Velocity Angle between the current and previous time points in radians; dx, dy, and dz are the changes in the x-, y-, and z-coordinates respectively of the detected object between the current and previous time points; and dt is the time between frames.

Type: Morphology, Per Time Point

The Diffusion Coefficient is a proportionality constant between the flux due to diffusion and the driving force for that diffusion, which is typically concentration. The Diffusion Coefficient (D) is calculated using the equation below, where t0 is the time when the track first appears. The Diffusion Coefficient is not calculated for the first time point in which the track is present.

Type: Morphology, Per Time Point

Direct Line Length is the Euclidean distance between where the object was when the track first appeared and where the object is at the current time point. Direct Line Length is not calculated for the first time point in which the track is present. In the figure below, Direct Line Length at time t is the distance a.

Type: Position, Per Time Point

Direct Line Velocity depends on the object’s current position, the object’s position at the time when its track first appears, and the amount of time that the track has existed up to the current time. Direct Line Velocity is calculated according to the equation below, where t0 is the time when the track first appears. As with Direct Line Length, Direct Line Velocity is not calculated for the first time point in which the track is present.

Type: Position, Per Time Point

Direct Line Velocity Squared is the square of the velocity of the object based on the object’s current position, the object’s position at the time when its track first appears, and the amount of time that the track has existed up to the current time. Direct Line Velocity is calculated according to the equation below, where t0 is the time when the track first appears. Direct Line Velocity Squared is not calculated for the first time point in which the track is present.

Type: Position, Over All Time

First Frame is the frame on which the track first appears. If a track is present on the very first frame, First Frame is equal to zero (0).

Type: Morphology, Per Time Point

Instantaneous Directedness is the cosine of the Velocity Angle (θ at time t in the figure below) and is calculated using the equation below. Velocity Angle is measured in degrees relative to the x-axis.

Type: Morphology, Per Time Point

Interval Length is the Euclidean distance between the object’s current position and the position of the object at the start of its lineage. If the track is not a child track, Interval Length is equal to Direct Line Length.

Type: Position, Over All Time

Last Frame is the last frame on which the track existed over the entire duration of the dataset. The first frame of the dataset is considered frame zero (0).

Type: Intensity, Per Time Point

Mask Color is the integer-valued color assigned to the object by the connected-components algorithm. Each object at each time point is expected to have a unique Mask Color value.

Type: Position, Over All Time

Max Velocity Magnitude is the maximum of the Velocity Magnitude measurements for the track over the duration that the track exists.

Type: Morphology, Over All Time

Mean Sphericity is the mean of the Sphericity measurements for the track over the duration that the track exists.

Type: Position, Per Time Point

Mean Square Displacement is the mean of the squared displacements from the position of the track at its earliest time point to it position at each time point up to the current time point. In the equation below, n0 is equal to the First Frame of the track and nc is the current frame number.

Type: Morphology, Over All Time

Mean Surface Area is the mean of the Surface Area measurements for the track over the duration that the track exists.

Type: Position, Over All Time

Mean Velocity is the Path Length (a+b+c+d+e for the example shown below) divided by the total time that the track exists.

Type: Position, Over All Time

Mean Velocity Magnitude is the mean of the Velocity Magnitude measurements for the track over the duration that the track exists.

Type: Morphology, Over All Time

Mean Volume is the mean of the Volume measurements for the track over the duration that the track exists.

Type: Position, Over All Time

Min Velocity Magnitude is the minimum of the Velocity Magnitude measurements for the track over the duration that the track exists.

Type: Morphology, Over All Time

Overall Directedness is the cosine of the Straight Line Velocity Angle (θ in the figure below).

Type: Morphology, Over All Time

Path Length is the distance traveled by the object along its trajectory over the entire duration of the track. Path Length is calculated as the sum of the Euclidean distances between the object’s positions at sequential time points, which is a+b+c+d+e for the example shown below.

Type: Position, Over All Time

Std Dev Velocity Magnitude is the standard deviation of the Velocity Magnitude measurements for the track over the duration that the track exists.

Type: Morphology, Over All Time

Straight Line Velocity Angle is the angle of the object’s velocity based on the object’s position on the first and last frames of its track. Straight Line Velocity Angle is the planar angle between the straight line velocity vector and the x-axis in degrees. In the example below, the Straight Line Velocity Angle is θ.

Type: Morphology, Over All Time

Tortuosity is a measure of twist in the track calculated as the Path Length (a+b+c+d+e for the example below) divided by the Euclidean distance between the endpoints of the track (f for the example below).

Type: Position, Over All Time

Total Frames is the number of frames on which the track exists.

Type: Position, Over All Time

Total Time is the duration over which the track exists.

Type: Intensity, Over All Time

Track Max Intensity for a given channel is the mean of the Max Intensity measurements for that channel and track over the duration that the track exists. The image channel for the measurement is indicated in the measurement name; for example, the Track Max Intensity for a channel named “GFP” is called “Track Max Intensity (GFP)” or “Track Max Intensity - GFP.”

Type: Intensity, Over All Time

Track Mean Intensity for a given channel is the mean of the Mean Intensity measurements for that channel and track over the duration that the track exists. The image channel for the measurement is indicated in the measurement name; for example, the Track Mean Intensity for a channel named “GFP” is called “Track Mean Intensity (GFP)” or “Track Mean Intensity - GFP.”

Type: Intensity, Over All Time

Track Min Intensity for a given channel is the mean of the Min Intensity measurements for that channel and track over the duration that the track exists. The image channel for the measurement is indicated in the measurement name; for example, the Track Min Intensity for a channel named “GFP” is called “Track Min Intensity (GFP)” or “Track Max Intensity - GFP.”

Type: Intensity, Over All Time

Track Std Dev Intensity for a given channel is the mean of the Std. Dev. Intensity measurements for that channel and track over the duration that the track exists. The image channel for the measurement is indicated in the measurement name; for example, the Track Std Dev Intensity for a channel named “GFP” is called “Track Std Dev Intensity (GFP)” or “Track Std Dev Intensity - GFP.”

Type: Position, Over All Time

Track Straight Line Velocity is the object’s velocity based on the object’s position on the first and last frames of its track and the duration of its track. Track Straight Line Velocity is the Euclidean distance between the endpoints of the track (a in the example below) divided by the Total Time of the track.

Type: Intensity, Over All Time

Track Total Intensity for a given channel is the mean of the Total Intensity measurements for that channel and track over the duration that the track exists. The image channel for the measurement is indicated in the measurement name; for example, the Track Total Intensity for a channel named “GFP” is called “Track Total Intensity (GFP)” or “Track Total Intensity - GFP.”

Type: Morphology, Per Time Point

Velocity Angle is the planar angle between the velocity vector at the current time point, which is estimated using the object's position at the current and previous time points and the time between frames (Δt), and the x-axis in degrees. This measurement is empty on the first time point of a track. In the example below, the Velocity Angle at time t is θ.

Type: Position, Per Time Point

Velocity Magnitude is the magnitude of the velocity vector at the current time point, which is estimated using the object's position at the current and previous time points and the time between frames (Δt). This measurement is empty on the first time point of a track but uses the position of the parent track if there was a lineage split between the current and previous frames.

Type: Position, Over All Time

Velocity Magnitude Variation is the variation in Velocity Magnitude over the duration of the track.

Lineage

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

Type: Count, Per Time Point

Current Lineage Track Count is the number of tracks in the lineage up to the current time point.

Type: Position, Over All Time

Lineage First Frame is the first frame on which the lineage appears; in other words, Lineage First Frame is the earliest frame on which the current track or any of its ancestors appears. The first frame of the dataset is considered frame zero (0).

Type: Position, Over All Time

Lineage First Split Time is the earliest time when the track or any of its ancestors split.

Type: Position, Over All Time

Lineage Last Frame is the last frame on which the lineage appears; in other words, Lineage Last Frame is the latest frame on which any track in the lineage to which the track belongs appears. The first frame of the dataset is considered frame zero (0).

Type: Morphology, Over All Time

Lineage Length is the number of frames over which the lineage extends.

Type: Morphology, Over All Time

Max Lineage Track Length is the duration of the longest track in the lineage to which the track belongs.

Type: Count, Over All Time

Max Track Generation is the maximum number of generations in the lineage to which the track belongs; in other words, this is the maximum number of tracks in a line of descent from the root track to a leaf track (a track with no children).

Type: Morphology, Over All Time

Mean Lineage Track Length is the mean duration of tracks in the lineage to which the track belongs.

Type: Count, Over All Time

Mean Track Generation is the mean number of generations in the lineage to which the track belongs; in other words, this is the mean number of tracks in a line of descent from the root track to a leaf track (a track with no children).

Type: Morphology, Over All Time

Min Lineage Track Length is the duration of the shortest (in time) track in the lineage to which the track belongs.

Type: Count, Over All Time

Min Track Generation is the smallest number of tracks in a line of descent from the root track to a leaf track (a track with no children) in the lineage to which the track belongs.

Type: Count, Over All Time

Total Childless Track Count is the total number of tracks that do not have children in the lineage to which the track belongs.

Type: Count, Over All Time

Total Lineage Track Count is the total number of tracks in the lineage to which the track belongs.

On this page:

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.

Type: Morphology, Per Time Point

Bounding Depth is the depth (extent in Z) of the bounding box for the entire neuron.

Type: Morphology, Per Time Point

Bounding Height is the height (extent in Y) of the bounding box for the entire neuron.

Type: Morphology, Per Time Point

Bounding Width is the width (extent in X) of the bounding box for the entire neuron.

Type: Position, Per Time Point

Centroid X is the x-coordinate of the center of the neuron’s bounding box.

Type: Position, Per Time Point

Centroid Y is the y-coordinate of the center of the neuron’s bounding box.

Type: Position, Per Time Point

Centroid Z is the z-coordinate of the center of the neuron’s bounding box.

Type: Count, Per Time Point

Dendrite Count is the total number of dendrite trees that the neuron has, which is equal to the number of dendrite segments that are directly connected to the soma.

Type: Morphology, Per Time Point

Fractal Dimension is the slope of the linear regression line for the log-log plot of Total Path Length vs. Straight Center Line Length (Euclidean distance between endpoints) for all dendrite segments making up the neuron.

Type: Position, Per Time Point

Max Dendrite Branch Euclidean Distance To Root is the maximum of the dendrite-branch-Euclidean-distance-to-root measurements for all dendrite segments belonging to the neuron. The dendrite branch Euclidean distance to root for a dendrite segment is the Euclidean distance from the endpoint of the dendrite segment, which is either a terminal point or a bifurcation point, to the root point (dendrite point that is connected to the soma) of the dendrite tree to which the dendrite segment belongs. In the example below, the dendrite branch Euclidean distance to root for “Dendrite Segment 3” is a.

Type: Count, Per Time Point

Max Dendrite Branch Generation is the highest number of generations in a lineage from a dendrite segment back to its or its ancestor’s connection to the soma for the entire neuron. A dendrite segment that is directly connected to the soma has a dendrite branch generation of zero (0). In the example below, dendrite segments are color-coded by their generation, which is given in the same color.

Type: Morphology, Per Time Point

Max Dendrite Branch Local Bifurcation Angle is the maximum dendrite branch local bifurcation angle for all bifurcations in the neuron. Dendrite branch local bifurcation angle is the angle formed by the bifurcation point and the two dendrite points (one on each child dendrite segment) that are directly connected to the bifurcation point. This angle is given in degrees and is represented by θ in the figure below.

Type: Morphology, Per Time Point

Max Dendrite Branch Mean Diameter is the maximum of the Mean Diameters of all dendrite segments belonging to the neuron.

Type: Count, Per Time Point

Max Dendrite Branch Node Count is the largest dendrite branch node count of all dendrite segments belonging to the neuron. Dendrite branch node count is the number of dendrite points (nodes) making up a single dendrite segment.

Type: Morphology, Per Time Point

Max Dendrite Branch Partition Asymmetry is the maximum dendrite branch partition asymmetry of all dendrite segments belonging to the neuron. Dendrite branch partition asymmetry is a measure of dendrite tree asymmetry that is based on the number of terminal points in each sub-tree extending from a bifurcation point. Dendrite branch partition asymmetry is calculated for each dendrite segment using the equation below, where T1 is the number of terminal points in the first sub-tree and T2 is the number of terminal points in the second sub-tree. For the example below the equation, the left sub-tree extending from “Dendrite Segment 2” has two (2) terminal points (circled in blue), while the right sub-tree has three (3) terminal points (circled in red); letting the left sub-tree be considered the first sub-tree and the right sub-tree be considered the second sub-tree, T1 is 2 and T2 is 3 for “Dendrite Segment 2.”

Type: Morphology, Per Time Point

Max Dendrite Branch Path Length is the longest Total Path Length of a dendrite segment in the neuron. Total Path Length for a dendrite segment is the sum of all Euclidean distances between adjacent dendrite points (nodes) making up the dendrite segment.

Type: Morphology, Per Time Point

Max Dendrite Branch Path Length To Root is the maximum dendrite branch path length to root for all dendrite segments belonging to the neuron and is equal to the maximum Longest Path Length of all dendrite trees belonging to the neuron. Dendrite branch path length to root for a dendrite segment is the path length from the endpoint of the dendrite segment back to its or its ancestor’s connection to the soma: it is the sum of the Total Path Lengths of the dendrite segment, its parent dendrite segment, its grandparent dendrite segment, and so on back to the root (ancestor that is directly connected to the soma). In the figure below, the dendrite branch path length to root for “Dendrite Segment 3” is represented by the length a.

Type: Morphology, Per Time Point

Max Dendrite Branch Ralls' Ratio is the maximum of the Ralls' ratios at each bifurcation in the neuron. Ralls' ratio at a bifurcation is calculated according to the equation below, where da is the diameter of the dendrite point that is connected to the bifurcation point on one of the child segments, db is the diameter of the dendrite point that is connected to the bifurcation point on the other child segment, and dp is the diameter of the bifurcation point on the parent segment.

Type: Morphology, Per Time Point

Max Dendrite Branch Remote Bifurcation Angle is the maximum of the dendrite branch remote bifurcation angles for all bifurcations belonging to the neuron. Dendrite branch remote bifurcation angle is the angle formed by the bifurcation point and the endpoints of the two (2) child dendrite segments extending from the bifurcation point. This angle is given in degrees and is represented by θ in the example below.

Type: Morphology, Per Time Point

Max Dendrite Branch Surface Area is the maximum of the Surface Areas of all dendrite segments belonging to the neuron.

Type: Morphology, Per Time Point

Max Dendrite Branch Tortuosity is the maximum of the Tortuosities of all dendrite segments belonging to the neuron.

Type: Morphology, Per Time Point

Max Dendrite Branch Volume is the maximum of the Volumes of all dendrite segments belonging to the neuron.

Type: Position, Per Time Point

Mean Dendrite Branch Euclidean Distance To Root is the mean of the dendrite-branch-Euclidean-distance-to-root measurements for all dendrite segments belonging to the neuron. The dendrite branch Euclidean distance to root for a dendrite segment is the Euclidean distance from the endpoint of the dendrite segment, which is either a terminal point or a bifurcation point, to the root point (dendrite point that is connected to the soma) of the dendrite tree to which the dendrite segment belongs. In the example below, the dendrite branch Euclidean distance to root for “Dendrite Segment 3” is a.

Type: Count, Per Time Point

Mean Dendrite Branch Generation is the mean dendrite branch generation of all dendrite segments belonging to the neuron. A dendrite segment that is directly connected to the soma has a dendrite branch generation of zero (0). In the example below, dendrite segments are color-coded by their generation, which is given in the same color.

Type: Morphology, Per Time Point

Mean Dendrite Branch Local Bifurcation Angle is the mean dendrite branch local bifurcation angle for all bifurcations in the neuron. Dendrite branch local bifurcation angle is the angle formed by the bifurcation point and the two dendrite points (one on each child dendrite segment) that are directly connected to the bifurcation point. This angle is given in degrees and is represented by θ in the figure below.

Type: Morphology, Per Time Point

Mean Dendrite Branch Mean Diameter is the mean of the Mean Diameters of all dendrite segments belonging to the neuron.

Type: Count, Per Time Point

Mean Dendrite Branch Node Count is the mean of the dendrite branch node counts of all dendrite segments belonging to the neuron. Dendrite branch node count is the number of dendrite points (nodes) making up a single dendrite segment.

Type: Morphology, Per Time Point

Mean Dendrite Branch Partition Asymmetry is the mean of the dendrite branch partition asymmetries of all dendrite segments belonging to the neuron. Dendrite branch partition asymmetry is a measure of dendrite tree asymmetry that is based on the number of terminal points in each sub-tree extending from a bifurcation point. Dendrite branch partition asymmetry is calculated for each dendrite segment using the equation below, where T1 is the number of terminal points in the first sub-tree and T2 is the number of terminal points in the second sub-tree. For the example below the equation, the left sub-tree extending from “Dendrite Segment 2” has two (2) terminal points (circled in blue), while the right sub-tree has three (3) terminal points (circled in red); letting the left sub-tree be considered the first sub-tree and the right sub-tree be considered the second sub-tree, T1 is 2 and T2 is 3 for “Dendrite Segment 2.”

Type: Morphology, Per Time Point

Mean Dendrite Branch Path Length is the mean of the Total Path Lengths of all dendrite segments belonging to the neuron. Total Path Length for a dendrite segment is the sum of all Euclidean distances between adjacent dendrite points (nodes) making up the dendrite segment.

Type: Morphology, Per Time Point

Mean Dendrite Branch Path Length To Root is the mean dendrite branch path length to root for all dendrite segments belonging to the neuron. Dendrite branch path length to root for a dendrite segment is the path length from the endpoint of the dendrite segment back to its or its ancestor’s connection to the soma: it is the sum of the Total Path Lengths of the dendrite segment, its parent dendrite segment, its grandparent dendrite segment, and so on back to the root (ancestor that is directly connected to the soma). In the figure below, the dendrite branch path length to root for “Dendrite Segment 3” is represented by the length a.

Type: Morphology, Per Time Point

Mean Dendrite Branch Ralls' Ratio is the mean of the Ralls' ratios at each bifurcation in the neuron. Ralls' ratio at a bifurcation is calculated according to the equation below, where da is the diameter of the dendrite point that is connected to the bifurcation point on one of the child segments, db is the diameter of the dendrite point that is connected to the bifurcation point on the other child segment, and dp is the diameter of the bifurcation point on the parent segment.

Type: Morphology, Per Time Point

Mean Dendrite Branch Remote Bifurcation Angle is the mean of the dendrite branch remote bifurcation angles for all bifurcations in the neuron. Dendrite branch remote bifurcation angle is the angle formed by the bifurcation point and the endpoints of the two (2) child dendrite segments extending from the bifurcation point. This angle is given in degrees and is represented by θ in the example below.

Type: Morphology, Per Time Point

Mean Dendrite Branch Surface Area is the mean of the Surface Areas of all dendrite segments belonging to the neuron.

Type: Morphology, Per Time Point

Mean Dendrite Branch Tortuosity is the mean of the Tortuosities of all dendrite segments belonging to the neuron.

Type: Morphology, Per Time Point

Mean Dendrite Branch Volume is the mean of the Volumes of all dendrite segments belonging to the neuron.

Type: Position, Per Time Point

Min Dendrite Branch Euclidean Distance To Root is the minimum of the dendrite-branch-Euclidean-distance-to-root measurements for all dendrite segments belonging to the neuron. The dendrite branch Euclidean distance to root for a dendrite segment is the Euclidean distance from the endpoint of the dendrite segment, which is either a terminal point or a bifurcation point, to the root point (dendrite point that is connected to the soma) of the dendrite tree to which the dendrite segment belongs. In the example below, the dendrite branch Euclidean distance to root for “Dendrite Segment 3” is a.

Type: Count, Per Time Point

Min Dendrite Branch Generation is the smallest number of generations in a lineage from a dendrite segment back to its or its ancestor’s connection to the soma for the entire neuron. A dendrite segment that is directly connected to the soma has a dendrite branch generation of zero (0). In the example below, dendrite segments are color-coded by their generation, which is given in the same color.

Type: Morphology, Per Time Point

Min Dendrite Branch Local Bifurcation Angle is the minimum dendrite branch local bifurcation angle for all bifurcations in the neuron. Dendrite branch local bifurcation angle is the angle formed by the bifurcation point and the two dendrite points (one on each child dendrite segment) that are directly connected to the bifurcation point. This angle is given in degrees and is represented by θ in the figure below.

Type: Morphology, Per Time Point

Min Dendrite Branch Mean Diameter is the minimum of the Mean Diameters of all dendrite segments belonging to the neuron.

Type: Count, Per Time Point

Min Dendrite Branch Node Count is the minimum of the dendrite branch node counts of all dendrite segments belonging to the neuron. Dendrite branch node count is the number of dendrite points (nodes) making up a single dendrite segment.

Type: Morphology, Per Time Point

Min Dendrite Branch Partition Asymmetry is the minimum of the dendrite branch partition asymmetries of all dendrite segments belonging to the neuron. Dendrite branch partition asymmetry is a measure of dendrite tree asymmetry that is based on the number of terminal points in each sub-tree extending from a bifurcation point. Dendrite branch partition asymmetry is calculated for each dendrite segment using the equation below, where T1 is the number of terminal points in the first sub-tree and T2 is the number of terminal points in the second sub-tree. For the example below the equation, the left sub-tree extending from “Dendrite Segment 2” has two (2) terminal points (circled in blue), while the right sub-tree has three (3) terminal points (circled in red); letting the left sub-tree be considered the first sub-tree and the right sub-tree be considered the second sub-tree, T1 is 2 and T2 is 3 for “Dendrite Segment 2.”

Type: Morphology, Per Time Point

Min Dendrite Branch Path Length is the Total Path Length of the dendrite segment that has the shortest Total Path Length for the whole neuron. Total Path Length for a dendrite segment is the sum of all Euclidean distances between adjacent dendrite points (nodes) making up the dendrite segment.

Type: Morphology, Per Time Point

Min Dendrite Branch Path Length To Root is the minimum dendrite branch path length to root for all dendrite segments belonging to the neuron and is equal to the minimum Shortest Path Length of all dendrite trees belonging to the neuron. Dendrite branch path length to root for a dendrite segment is the path length from the endpoint of the dendrite segment back to its or its ancestor’s connection to the soma: it is the sum of the Total Path Lengths of the dendrite segment, its parent dendrite segment, its grandparent dendrite segment, and so on back to the root (ancestor that is directly connected to the soma). In the figure below, the dendrite branch path length to root for “Dendrite Segment 3” is represented by the length a.

Type: Morphology, Per Time Point

Min Dendrite Branch Ralls' Ratio is the minimum of the Ralls' ratios at each bifurcation in the neuron. Ralls' ratio at a bifurcation is calculated according to the equation below, where da is the diameter of the dendrite point that is connected to the bifurcation point on one of the child segments, db is the diameter of the dendrite point that is connected to the bifurcation point on the other child segment, and dp is the diameter of the bifurcation point on the parent segment.

Type: Morphology, Per Time Point

Min Dendrite Branch Remote Bifurcation Angle is the minimum of the dendrite branch remote bifurcation angles for all bifurcations in the neuron. Dendrite branch remote bifurcation angle is the angle formed by the bifurcation point and the endpoints of the two (2) child dendrite segments extending from the bifurcation point. This angle is given in degrees and is represented by θ in the example below.

Type: Morphology, Per Time Point

Min Dendrite Branch Surface Area is the minimum of the Surface Areas of all dendrite segments belonging to the neuron.

Type: Morphology, Per Time Point

Min Dendrite Branch Tortuosity is the minimum of the Tortuosities of all dendrite segments belonging to the neuron.

Type: Morphology, Per Time Point

Min Dendrite Branch Volume is the minimum of the Volumes of all dendrite segments belonging to the neuron.

Type: Count, Per Time Point

Number of Bifurcation is the total number of bifurcations in all dendrite trees of the neuron.

Type: Count, Per Time Point

Number of Branches is the total number of dendrite segments that belong to the neuron.

Type: Count, Per Time Point

Number of Terminal Tips is the total number of terminal tips for the neuron, which is equal to the total number of dendrite segments belonging to the neuron that have no child segments.

Type: Position, Per Time Point

Soma Skewness Euclidean Distance is the Euclidean distance between the Centroid of the soma and the Centroid of the entire neuron.

Type: Position, Per Time Point

Soma Skewness X is the difference between the x-coordinate of the Centroid of the soma and the x-coordinate of the Centroid of the entire neuron.

Type: Position, Per Time Point

Soma Skewness Y is the difference between the y-coordinate of the Centroid of the soma and the y-coordinate of the Centroid of the entire neuron.

Type: Position, Per Time Point

Soma Skewness Z is the difference between the z-coordinate of the Centroid of the soma and the z-coordinate of the Centroid of the entire neuron.

Type: Position, Per Time Point

Std Dev Dendrite Branch Euclidean Distance To Root is the standard deviation of the dendrite-branch-Euclidean-distance-to-root measurements for all dendrite segments belonging to the neuron. The dendrite branch Euclidean distance to root for a dendrite segment is the Euclidean distance from the endpoint of the dendrite segment, which is either a terminal point or a bifurcation point, to the root point (dendrite point that is connected to the soma) of the dendrite tree to which the dendrite segment belongs. In the example below, the dendrite branch Euclidean distance to root for “Dendrite Segment 3” is a.

Type: Count, Per Time Point

Std Dev Dendrite Branch Generation is the standard deviation of the dendrite branch generations of all dendrite segments belonging to the neuron. A dendrite segment that is directly connected to the soma has a dendrite branch generation of zero (0). In the example below, dendrite segments are color-coded by their generation, which is given in the same color.

Type: Morphology, Per Time Point

Std Dev Dendrite Branch Local Bifurcation Angle is the standard deviation of the dendrite branch local bifurcation angles for all bifurcations in the neuron. Dendrite branch local bifurcation angle is the angle formed by the bifurcation point and the two dendrite points (one on each child dendrite segment) that are directly connected to the bifurcation point. This angle is given in degrees and is represented by θ in the figure below.

Type: Morphology, Per Time Point

Std Dev Dendrite Branch Mean Diameter is the standard deviation of the Mean Diameters of all dendrite segments belonging to the neuron.

Type: Count, Per Time Point

Std Dev Dendrite Branch Node Count is the standard deviation of the dendrite branch node counts of all dendrite segments belonging to the neuron. Dendrite branch node count is the number of dendrite points (nodes) making up a single dendrite segment.

Type: Morphology, Per Time Point

Std Dev Dendrite Branch Partition Asymmetry is the standard deviation of the dendrite branch partition asymmetries of all dendrite segments belonging to the neuron. Dendrite branch partition asymmetry is a measure of dendrite tree asymmetry that is based on the number of terminal points in each sub-tree extending from a bifurcation point. Dendrite branch partition asymmetry is calculated for each dendrite segment using the equation below, where T1 is the number of terminal points in the first sub-tree and T2 is the number of terminal points in the second sub-tree. For the example below the equation, the left sub-tree extending from “Dendrite Segment 2” has two (2) terminal points (circled in blue), while the right sub-tree has three (3) terminal points (circled in red); letting the left sub-tree be considered the first sub-tree and the right sub-tree be considered the second sub-tree, T1 is 2 and T2 is 3 for “Dendrite Segment 2.”

Type: Morphology, Per Time Point

Std Dev Dendrite Branch Path Length is the standard deviation of the Total Path Lengths of all dendrite segments belonging to the neuron. Total Path Length for a dendrite segment is the sum of all Euclidean distances between adjacent dendrite points (nodes) making up the dendrite segment.

Type: Morphology, Per Time Point

Std Dev Dendrite Branch Path Length To Root is the standard deviation of the dendrite-branch-path-length-to-root measurements for all dendrite segments belonging to the neuron. Dendrite branch path length to root for a dendrite segment is the path length from the endpoint of the dendrite segment back to its or its ancestor’s connection to the soma: it is the sum of the Total Path Lengths of the dendrite segment, its parent dendrite segment, its grandparent dendrite segment, and so on back to the root (ancestor that is directly connected to the soma). In the figure below, the dendrite branch path length to root for “Dendrite Segment 3” is represented by the length a.

Type: Morphology, Per Time Point

Std Dev Dendrite Branch Ralls' Ratio is the standard deviation of the Ralls' ratios at each bifurcation in the neuron. Ralls' ratio at a bifurcation is calculated according to the equation below, where da is the diameter of the dendrite point that is connected to the bifurcation point on one of the child segments, db is the diameter of the dendrite point that is connected to the bifurcation point on the other child segment, and dp is the diameter of the bifurcation point on the parent segment.

Type: Morphology, Per Time Point

Std Dev Dendrite Branch Remote Bifurcation Angle is the standard deviation of the dendrite branch remote bifurcation angles for all bifurcations in the neuron. Dendrite branch remote bifurcation angle is the angle formed by the bifurcation point and the endpoints of the two (2) child dendrite segments extending from the bifurcation point. This angle is given in degrees and is represented by θ in the example below.

Type: Morphology, Per Time Point

Std Dev Dendrite Branch Surface Area is the standard deviation of the Surface Areas of all dendrite segments belonging to the neuron.

Type: Morphology, Per Time Point

Std Dev Dendrite Branch Tortuosity is the standard deviation of the Tortuosities of all dendrite segments belonging to the neuron.

Type: Morphology, Per Time Point

Std Dev Dendrite Branch Volume is the standard deviation of the Volumes of all dendrite segments belonging to the neuron.

Type: Position, Per Time Point

Total Dendrite Branch Euclidean Distance To Root is the sum of the dendrite-branch-Euclidean-distance-to-root measurements for all dendrite segments belonging to the neuron. The dendrite branch Euclidean distance to root for a dendrite segment is the Euclidean distance from the endpoint of the dendrite segment, which is either a terminal point or a bifurcation point, to the root point (dendrite point that is connected to the soma) of the dendrite tree to which the dendrite segment belongs. In the example below, the dendrite branch Euclidean distance to root for “Dendrite Segment 3” is a.

Type: Count, Per Time Point

Total Dendrite Branch Generation is the sum of the dendrite branch generations of all dendrite segments belonging to the neuron. A dendrite segment that is directly connected to the soma has a dendrite branch generation of zero (0). In the example below, dendrite segments are color-coded by their generation, which is given in the same color.

Type: Morphology, Per Time Point

Total Dendrite Branch Local Bifurcation Angle is the sum of the dendrite branch local bifurcation angles for all bifurcations in the neuron. Dendrite branch local bifurcation angle is the angle formed by the bifurcation point and the two dendrite points (one on each child dendrite segment) that are directly connected to the bifurcation point. This angle is given in degrees and is represented by θ in the figure below.

Type: Morphology, Per Time Point

Total Dendrite Branch Mean Diameter is the sum of the Mean Diameters of all dendrite segments belonging to the neuron.

Type: Count, Per Time Point

Total Dendrite Branch Node Count is the sum of the dendrite branch node counts of all dendrite segments belonging to the neuron. Dendrite branch node count is the number of dendrite points (nodes) making up a single dendrite segment.

Type: Morphology, Per Time Point

Total Dendrite Branch Partition Asymmetry is the sum of the dendrite branch partition asymmetries of all dendrite segments belonging to the neuron. Dendrite branch partition asymmetry is a measure of dendrite tree asymmetry that is based on the number of terminal points in each sub-tree extending from a bifurcation point. Dendrite branch partition asymmetry is calculated for each dendrite segment using the equation below, where T1 is the number of terminal points in the first sub-tree and T2 is the number of terminal points in the second sub-tree. For the example below the equation, the left sub-tree extending from “Dendrite Segment 2” has two (2) terminal points (circled in blue), while the right sub-tree has three (3) terminal points (circled in red); letting the left sub-tree be considered the first sub-tree and the right sub-tree be considered the second sub-tree, T1 is 2 and T2 is 3 for “Dendrite Segment 2.”

Type: Morphology, Per Time Point

Total Dendrite Branch Path Length is the sum of the Total Path Lengths of all dendrite segments belonging to the neuron. Total Path Length for a dendrite segment is the sum of all Euclidean distances between adjacent dendrite points (nodes) making up the dendrite segment.

Type: Morphology, Per Time Point

Total Dendrite Branch Path Length To Root is the sum of the dendrite-branch-path-length-to-root measurements for all dendrite segments belonging to the neuron. Dendrite branch path length to root for a dendrite segment is the path length from the endpoint of the dendrite segment back to its or its ancestor’s connection to the soma: it is the sum of the Total Path Lengths of the dendrite segment, its parent dendrite segment, its grandparent dendrite segment, and so on back to the root (ancestor that is directly connected to the soma). In the figure below, the dendrite branch path length to root for “Dendrite Segment 3” is represented by the length a.

Type: Morphology, Per Time Point

Total Dendrite Branch Ralls' Ratio is the sum of the Ralls' ratios at each bifurcation in the neuron. Ralls' ratio at a bifurcation is calculated according to the equation below, where da is the diameter of the dendrite point that is connected to the bifurcation point on one of the child segments, db is the diameter of the dendrite point that is connected to the bifurcation point on the other child segment, and dp is the diameter of the bifurcation point on the parent segment.

Type: Morphology, Per Time Point

Total Dendrite Branch Remote Bifurcation Angle is the sum of the dendrite branch remote bifurcation angles for all bifurcations in the neuron. Dendrite branch remote bifurcation angle is the angle formed by the bifurcation point and the endpoints of the two (2) child dendrite segments extending from the bifurcation point. This angle is given in degrees and is represented by θ in the example below.

Type: Morphology, Per Time Point

Total Dendrite Branch Surface Area is the sum of the Surface Areas of all dendrite segments belonging to the neuron.

Type: Morphology, Per Time Point

Total Dendrite Branch Tortuosity is the sum of the Tortuosities of all dendrite segments belonging to the neuron.

Type: Morphology, Per Time Point

Total Dendrite Branch Volume is the sum of the Volumes of all dendrite segments belonging to the neuron.

Type: Morphology, Per Time Point

Total Surface Area is the sum of the Surface Area of the soma and the Surface Areas of all dendrites.

Type: Morphology, Per Time Point

Total Volume is the sum of the Volume of the soma and the Volumes of all dendrites.

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.

Type: Count, Per Time Point

For dendrite trees, Bifurcation Count is the number of bifurcations, or branch points, in the dendrite tree. For dendrite segments, Bifurcation Count is the number of bifurcations in the dendrite segment’s sub-trees plus 0.5 for the bifurcation at the end the dendrite segment; if the dendrite segment has no children, the Bifurcation Count is zero (0). In the example below, the Bifurcation Count for “Dendrite Segment 2” is 3.5 since “Dendrite Segment 2” has three (3) bifurcations in its sub-trees (circled in red) and a bifurcation at its end (circled in orange). The dendrite tree in the example below has a Bifurcation Count of five (5).

Type: Morphology, Per Time Point

Branch Angle is the local bifurcation angle for the dendrite segment, which is the smallest planar angle between vectors extending from the bifurcation point to dendrite points on each child segment that are directly connected to the bifurcation point. This angle is given in degrees and is represented by θ for “Dendrite Segment 1” in the figure below. This measurement is empty for dendrite segments that do not have children as well as for dendrite trees.

Type: Count, Per Time Point

For dendrite trees, Branch Count is the number of dendrite segments that make up the dendrite tree. For a dendrite segment, Branch Count is the total number of dendrite segments in the dendrite segment’s sub-trees, if they exist; if the dendrite segment has no children, Branch Count is zero (0).

Type: Count, Per Time Point

For a dendrite segment, Branch Order is the generation of the segment: the Branch Order of the root segment is zero (0), the Branch Order of the root segment’s children is one (1), the Branch Order of the root segment’s grandchildren is two (2), and so on. In the example below, dendrite segments are color-coded by their Branch Order, which is given in the same color. Branch Order is always zero (0) for dendrite trees.

Type: Morphology, Per Time Point

Longest Path Length for a dendrite tree is the longest path length from the root node to the end of a terminal branch. For dendrite segments, Longest Path Length is equal to Shortest Path Length, and both are equal to the sum of the Total Path Length of the dendrite segment and the Total Path Lengths of each of its ancestors back to the root segment.

Type: Count, Per Time Point

For dendrite trees, Max Child Branch Order is the highest Branch Order, or generation, of a dendrite segment in the dendrite tree. For dendrite segments, Max Child Branch Order is the highest Branch Order of a dendrite segment in either of the segment’s sub-trees; if a dendrite segment has no children, its Max Child Branch Order is blank. In the example below, dendrite segments are color-coded by their Branch Order, which is given in the same color. The Max Child Branch Order for “Dendrite Segment 3” is three (3) because “Dendrite Segment 3” has only two (2) child segments, both of which are third (3rd) generation. The Max Child Branch Order for the dendrite tree is four (4).

Type: Morphology, Per Time Point

For dendrite trees, Max Tortuosity is the maximum tortuosity of a dendrite segment in the dendrite tree. The tortuosity of a dendrite segment is the path length (Total Path Length) of the dendrite segment divided by the Euclidean distance between the endpoints of the segment. For dendrite segments, Max Tortuosity, Min Tortuosity, and Mean Tortuosity are all equal to the tortuosity of the segment.

Type: Morphology, Per Time Point

Mean Diameter is the mean diameter of all dendrite points composing the dendrite tree or segment.

Type: Morphology, Per Time Point

For dendrite trees, Mean Tortuosity is the mean of the tortuosities of all dendrite segments in the dendrite tree. The tortuosity of a dendrite segment is the path length (Total Path Length) of the dendrite segment divided by the Euclidean distance between the endpoints of the segment. For dendrite segments, Max Tortuosity, Min Tortuosity, and Mean Tortuosity are all equal to the tortuosity of the segment.

Type: Morphology, Per Time Point

For dendrite trees, Min Tortuosity is the minimum tortuosity of a dendrite segment in the dendrite tree. The tortuosity of a dendrite segment is the path length (Total Path Length) of the dendrite segment divided by the Euclidean distance between the endpoints of the segment. For dendrite segments, Max Tortuosity, Min Tortuosity, and Mean Tortuosity are all equal to the tortuosity of the segment.

Type: Morphology, Per Time Point

Neuron ID is the number of the neuron to which the dendrite tree or dendrite segment belongs. If the tree is not connected to a soma, and therefore not part of a neuron object, the Neuron ID is blank for the tree and its segments.

Type: Morphology, Per Time Point

Shortest Path Length for a dendrite tree is the shortest path length from the root node to the end of a terminal branch. For dendrite segments, Shortest Path Length is equal to Longest Path Length, and both are equal to the sum of the Total Path Length of the dendrite segment and the Total Path Lengths of each of its ancestors back to the root segment.

Type: Count, Per Time Point

For dendrite trees, Spine Count is the total number of spines on the dendrite tree. For a dendrite segment, Spine Count is the total number of spines on the dendrite segment.

Type: Morphology, Per Time Point

For dendrite trees, Std. Dev. is the standard deviation of the tortuosities of all dendrite segments composing the dendrite tree. The tortuosity of a dendrite segment is the path length (Total Path Length) of the dendrite segment divided by the Euclidean distance between the endpoints of the segment. For dendrite segments, Std. Dev. Tortuosity is 0 since only one tortuosity is calculated for the dendrite segment..

Type: Morphology, Per Time Point

Total Path Length for a dendrite segment is the sum of all Euclidean distances between adjacent dendrite points (nodes) making up the dendrite segment. For a dendrite tree, Total Path Length is the sum of the Total Path Lengths of all dendrite segments making up the dendrite tree.

Type: Morphology, Per Time Point

Tree ID is the number of the dendrite tree to which a dendrite segment belongs. For dendrite trees, the Tree ID is generally the same as the number in the dendrite-tree name.

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.

Type: Morphology, Per Time Point

Branch Angle for a spine is the planar angle (in degrees) between the vector that extends from the first to last points of the parent dendrite segment and the vector that extends from the first to last points of the center line of the spine neck. Branch Angle is represented by θ for one of the spines in the example below.

Type: Morphology, Per Time Point

Head Neck Length Ratio is the ratio of the Center Line Length of the spine head to the Center Line Length of the spine neck.

Type: Morphology, Per Time Point

Head Neck Volume Ratio is the ratio of the Volume of the spine head to the Volume of the spine neck.

Type: Morphology, Per Time Point

Length To Head Diameter Ratio is the ratio of the Total Spine Length to the Spine Head Diameter.

Type: Morphology, Per Time Point

Neuron ID is the number of the neuron to which the spine belongs. Neuron ID is blank for spines on dendrite trees that are not connected to somas.

Type: Morphology, Per Time Point

Segment ID is the number of the dendrite segment that the spine is on.

Type: Morphology, Per Time Point

Spine Convex Hull Volume Ratio is the ratio of the Convex Hull Volume of the spine head to the Convex Hull Volume of the spine neck. Convex Hull Volume of a mesh is the volume of the smallest convex set shape that contains the mesh.

Type: Morphology, Per Time Point

Spine Diameter Ratio is the ratio of the Spine Head Diameter to an estimation of the spine neck diameter that depends on the Volume of the spine neck and the Center Line Length of the spine neck.

Type: Morphology, Per Time Point

Spine Head Diameter is estimated as the longest axis of a cross-section of the spine head that is perpendicular to the center line. If estimation by the previous method fails, Spine Head Diameter is calculated with the equation below.

Type: Morphology, Per Time Point

Spine Surface Area Ratio is the ratio of the Surface Area of the spine head to the Surface Area of the spine neck.

Type: Morphology, Per Time Point

Spine Tortuosity is a measure of the twist in the spine that is calculated as the length of the spine’s center line (Total Spine Length) divided by the Euclidean distance between the endpoints of the center line.

Type: Morphology, Per Time Point

Total Spine Length is the length of the spine’s center line, which extends from the base of the spine to the top of the spine head.

Type: Morphology, Per Time Point

Total Spine Surface Area is the sum of the Surface Area of the spine head and the Surface Area of the spine neck.

Type: Morphology, Per Time Point

Total Spine Volume is the sum of the Volume of the spine head and the Volume of the spine neck.

Type: Morphology, Per Time Point

Tree ID is the number of the dendrite tree that the spine is on.

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.

Type: Morphology, Per Time Point

Area to Contained Vesicle Area Ratio is the ratio of the Area of the membrane to the sum of the Areas of all vesicles on the membrane.

Type: Position, Per Time Point

Cell ID is the number of the cell object to which the membrane is associated. Generally, the Cell ID is the same as the number in the membrane name.

Type: Count, Per Time Point

Contained Vesicle Count is the total number of vesicles on the membrane.

Type: Morphology, Per Time Point

Max Contained Vesicle Area is the maximum of the Areas of all vesicles on the membrane.

Type: Position, Per Time Point

Max Contained Vesicle Distance to Center is the longest Euclidean distance between the Centroid of a vesicle on the membrane and the Centroid of the membrane.

Type: Intensity, Per Time Point

Max Contained Vesicle Intensity is the maximum intensity of the given channel over all pixels contained by vesicles on the membrane. The image channel for the measurement is indicated in the measurement name; for example, the Max Contained Vesicle Intensity for a channel named “GFP” is called “Max Contained Vesicle Intensity (GFP)” or “Max Contained Vesicle Intensity - GFP.”

Type: Position, Per Time Point

Max Vesicle Center of Mass X is the maximum of the x-coordinates of the Centers of Mass of all vesicles on the membrane.

Type: Position, Per Time Point

Max Vesicle Center of Mass Y is the maximum of the y-coordinates of the Centers of Mass of all vesicles on the membrane.

Type: Morphology, Per Time Point

Mean Contained Vesicle Area is the mean Area of vesicles on the membrane.

Type: Position, Per Time Point

Mean Contained Vesicle Distance to Center is the mean Euclidean distance between the Centroid of a vesicle on the membrane and the Centroid of the membrane.

Type: Intensity, Per Time Point

Mean Contained Vesicle Intensity is the mean of the Mean Intensities for the given channel for all vesicles on the membrane. The image channel for the measurement is indicated in the measurement name; for example, the Mean Contained Vesicle Intensity for a channel named “GFP” is called “Mean Contained Vesicle Intensity (GFP)” or “Mean Contained Vesicle Intensity - GFP.”

Type: Position, Per Time Point

Mean Vesicle Center of Mass X is the mean of the x-coordinates of the Centers of Mass of all vesicles on the membrane.

Type: Position, Per Time Point

Mean Vesicle Center of Mass Y is the mean of the y-coordinates of the Centers of Mass of all vesicles on the membrane.

Type: Morphology, Per Time Point

Min Contained Vesicle Area is the minimum of the Areas of all vesicles on the membrane.

Type: Position, Per Time Point

Min Contained Vesicle Distance to Center is the shortest Euclidean distance between the Centroid of a vesicle on the membrane and the Centroid of the membrane.

Type: Intensity, Per Time Point

Min Contained Vesicle Intensity is the minimum intensity of the given channel over all pixels contained by vesicles on the membrane. The image channel for the measurement is indicated in the measurement name; for example, the Min Contained Vesicle Intensity for a channel named “GFP” is called “Min Contained Vesicle Intensity (GFP)” or “Min Contained Vesicle Intensity - GFP.”

Type: Position, Per Time Point

Min Vesicle Center of Mass X is the minimum of the x-coordinates of the Centers of Mass of all vesicles on the membrane.

Type: Position, Per Time Point

Min Vesicle Center of Mass Y is the minimum of the y-coordinates of the Centers of Mass of all vesicles on the membrane.

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.

Type: Position, Per Time Point

Cell ID is the number of the cell object to which the membrane is associated. Generally, the Cell ID is the same as the number in the membrane name.

Type: Count, Per Time Point

Contained Vesicle Count is the total number of vesicles on the membrane.

Type: Position, Per Time Point

Max Contained Vesicle Distance to Center is the longest Euclidean distance between the Centroid of a vesicle on the membrane and the Centroid of the membrane.

Type: Intensity, Per Time Point

Max Contained Vesicle Intensity is the maximum intensity of the given channel over all voxels contained by vesicles on the membrane. The image channel for the measurement is indicated in the measurement name; for example, the Max Contained Vesicle Intensity for a channel named “GFP” is called “Max Contained Vesicle Intensity (GFP)” or “Max Contained Vesicle Intensity - GFP.”

Type: Morphology, Per Time Point

Max Contained Vesicle Volume is the maximum of the Volumes of all vesicles on the membrane.

Type: Position, Per Time Point

Max Vesicle Center of Mass X is the maximum of the x-coordinates of the Centers of Mass of all vesicles on the membrane.

Type: Position, Per Time Point

Max Vesicle Center of Mass Y is the maximum of the y-coordinates of the Centers of Mass of all vesicles on the membrane.

Type: Position, Per Time Point

Max Vesicle Center of Mass Z is the maximum of the z-coordinates of the Centers of Mass of all vesicles on the membrane.

Type: Position, Per Time Point

Mean Contained Vesicle Distance to Center is the mean Euclidean distance between the Centroid of a vesicle on the membrane and the Centroid of the membrane.

Type: Intensity, Per Time Point

Mean Contained Vesicle Intensity is the mean of the Mean Intensities for the given channel for all vesicles on the membrane. The image channel for the measurement is indicated in the measurement name; for example, the Mean Contained Vesicle Intensity for a channel named “GFP” is called “Mean Contained Vesicle Intensity (GFP)” or “Mean Contained Vesicle Intensity - GFP.”

Type: Morphology, Per Time Point

Mean Contained Vesicle Volume is the mean Volume of vesicles on the membrane.

Type: Position, Per Time Point

Mean Vesicle Center of Mass X is the mean of the x-coordinates of the Centers of Mass of all vesicles on the membrane.

Type: Position, Per Time Point

Mean Vesicle Center of Mass Y is the mean of the y-coordinates of the Centers of Mass of all vesicles on the membrane.

Type: Position, Per Time Point

Mean Vesicle Center of Mass Z is the mean of the z-coordinates of the Centers of Mass of all vesicles on the membrane.

Type: Position, Per Time Point

Min Contained Vesicle Distance to Center is the shortest Euclidean distance between the Centroid of a vesicle on the membrane and the Centroid of the membrane.

Type: Intensity, Per Time Point

Min Contained Vesicle Intensity is the minimum intensity of the given channel over all voxels contained by vesicles on the membrane. The image channel for the measurement is indicated in the measurement name; for example, the Min Contained Vesicle Intensity for a channel named “GFP” is called “Min Contained Vesicle Intensity (GFP)” or “Min Contained Vesicle Intensity - GFP.”

Type: Morphology, Per Time Point

Min Contained Vesicle Volume is the minimum of the Volumes of all vesicles on the membrane.

Type: Position, Per Time Point

Min Vesicle Center of Mass X is the minimum of the x-coordinates of the Centers of Mass of all vesicles on the membrane.

Type: Position, Per Time Point

Min Vesicle Center of Mass Y is the minimum of the y-coordinates of the Centers of Mass of all vesicles on the membrane.

Type: Position, Per Time Point

Min Vesicle Center of Mass Z is the minimum of the z-coordinates of the Centers of Mass of all vesicles on the membrane.

Type: Morphology, Per Time Point

Volume to Contained Vesicle Volume Ratio is the ratio of the Volume of the membrane to the sum of the Volumes of all vesicles on the membrane.

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.

Type: Morphology, Per Time Point

% Overlapped is the percentage of the vesicle area that is overlapped with its parent, which is a cell membrane, cytoplasm, nuclear membrane, or nucleus.

Type: Morphology, Per Time Point

Area Overlapped is the area of the vesicle that is overlapped with its parent, which is a cell membrane, cytoplasm, nuclear membrane, or nucleus.

Type: Position, Per Time Point

Cell ID is the number of the cell object to which the vesicle belongs. This measurement is empty for vesicles that are not within a cell.

Type: Position, Per Time Point

Distance to Center of Mass of Cell is the Euclidean distance between the Center of Mass of the vesicle and the Center of Mass of the cell to which it belongs. If the vesicle does not belong to a cell, Distance to Center of Mass of Cell is the Euclidean distance between the Center of Mass of the vesicle and the Center of Mass of the cell with the nearest cell membrane.

Type: Position, Per Time Point

Distance to Center of Mass of Nucleus is the Euclidean distance between the Center of Mass of the vesicle and the Center of Mass of its cell’s nucleus. If the vesicle does not belong to a cell, Distance to Center of Mass of Nucleus is the Euclidean distance between the Center of Mass of the vesicle and the Center of Mass of the nucleus with the nearest nuclear membrane.

Type: Position, Per Time Point

Distance to Nearest Edge of Cell is the Euclidean distance between the Centroid of the vesicle and the nearest vertex of the cell membrane to which the vesicle is associated. If the vesicle does not belong to a cell, Distance to Nearest Edge of Cell is the Euclidean distance between the Centroid of the vesicle and the nearest vertex of any cell membrane.

Type: Position, Per Time Point

Distance to Nearest Edge of Nucleus is the Euclidean distance between the Centroid of the vesicle and the nearest vertex of the associated nuclear membrane. If the vesicle does not belong to a cell, Distance to Nearest Edge of Nucleus is the Euclidean distance between the Centroid of the vesicle and the nearest vertex of any nuclear membrane.

Type: Position, Per Time Point

Is In Cytoplasm is a Boolean value that indicates whether the vesicle is in a cytoplasm (1) or not (0).

Type: Position, Per Time Point

Is In Nucleus is a Boolean value that indicates whether the vesicle is in a nucleus (1) or not (0).

Type: Position, Per Time Point

Is On Cell Membrane is a Boolean value that indicates whether the vesicle is on a cell membrane (1) or not (0).

Type: Position, Per Time Point

Is On Nuclear Membrane is a Boolean value that indicates whether the vesicle is on a nuclear membrane (1) or not (0).

Type: Count, Per Time Point

Relations on Frame is equal to one (1) if the vesicle belongs to a cell and zero (0) otherwise. If the vesicle has a relation, its parent is the cell membrane, cytoplasm, nuclear membrane, or nucleus.

Type: Position, Per Time Point

Relative Center of Mass Distance is the Euclidean distance between the Center of Mass of the vesicle and the Center of Mass of its parent, which is a cell membrane, cytoplasm, nuclear membrane, or nucleus.

Type: Position, Per Time Point

Relative Center of Mass X Position is the difference between the x-coordinate of the vesicle’s Center of Mass and the x-coordinate of its parent’s Center of Mass. The vesicle’s parent (if it exists) is a cell membrane, cytoplasm, nuclear membrane, or nucleus.

Type: Position, Per Time Point

Relative Center of Mass Y Position is the difference between the y-coordinate of the vesicle’s Center of Mass and the y-coordinate of its parent’s Center of Mass. The vesicle’s parent (if it exists) is a cell membrane, cytoplasm, nuclear membrane, or nucleus.

Type: Position, Per Time Point

Relative Center of Mass Z Position is the difference between the z-coordinate of the vesicle’s Center of Mass and the z-coordinate of its parent’s Center of Mass. The vesicle’s parent (if it exists) is a cell membrane, cytoplasm, nuclear membrane, or nucleus.

Type: Position, Per Time Point

Relative Distance is the Euclidean distance between the Centroid of the vesicle and the Centroid of its parent, which is a cell membrane, cytoplasm, nuclear membrane, or nucleus.

Type: Position, Per Time Point

Relative X Position is the difference between the x-coordinate of the vesicle’s Centroid and the x-coordinate of its parent’s Centroid. The vesicle’s parent (if it exists) is a cell membrane, cytoplasm, nuclear membrane, or nucleus.

Type: Position, Per Time Point

Relative Y Position is the difference between the y-coordinate of the vesicle’s Centroid and the y-coordinate of its parent’s Centroid. The vesicle’s parent (if it exists) is a cell membrane, cytoplasm, nuclear membrane, or nucleus.

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.

Type: Position, Per Time Point

Cell ID is the number of the cell object to which the vesicle belongs. This measurement is empty for vesicles that are not within a cell.

Type: Position, Per Time Point

Distance to Center of Mass of Cell is the Euclidean distance between the Center of Mass of the vesicle and the Center of Mass of the cell to which it belongs. If the vesicle does not belong to a cell, Distance to Center of Mass of Cell is the Euclidean distance between the Center of Mass of the vesicle and the Center of Mass of the cell with the nearest cell membrane.

Type: Position, Per Time Point

Distance to Center of Mass of Nucleus is the Euclidean distance between the Center of Mass of the vesicle and the Center of Mass of its cell’s nucleus. If the vesicle does not belong to a cell, Distance to Center of Mass of Nucleus is the Euclidean distance between the Center of Mass of the vesicle and the Center of Mass of the nucleus with the nearest nuclear membrane.

Type: Position, Per Time Point

Distance to Nearest Edge of Cell is the Euclidean distance between the Centroid of the vesicle and the nearest vertex of the cell membrane to which the vesicle is associated. If the vesicle does not belong to a cell, Distance to Nearest Edge of Cell is the Euclidean distance between the Centroid of the vesicle and the nearest vertex of any cell membrane. The lowest available level of detail of cell-membrane meshes is used for this measurement calculation.

Type: Position, Per Time Point

Distance to Nearest Edge of Nucleus is the Euclidean distance between the Centroid of the vesicle and the nearest vertex of the associated nuclear membrane. If the vesicle does not belong to a cell, Distance to Nearest Edge of Nucleus is the Euclidean distance between the Centroid of the vesicle and the nearest vertex of any nuclear membrane. The lowest available level of detail of nuclear-membrane meshes is used for this measurement calculation.

Type: Position, Per Time Point

Is In Cytoplasm is a Boolean value that indicates whether the vesicle is in a cytoplasm (1) or not (0).

Type: Position, Per Time Point

Is In Nucleus is a Boolean value that indicates whether the vesicle is in a nucleus (1) or not (0).

Type: Position, Per Time Point

Is On Cell Membrane is a Boolean value that indicates whether the vesicle is on a cell membrane (1) or not (0).

Type: Position, Per Time Point

Is On Nuclear Membrane is a Boolean value that indicates whether the vesicle is on a nuclear membrane (1) or not (0).

Type: Count, Per Time Point

Relations on Frame is equal to one (1) if the vesicle belongs to a cell and zero (0) otherwise. If the vesicle has a relation, its parent is the cell membrane, cytoplasm, nuclear membrane, or nucleus.

Type: Position, Per Time Point

Relative Center of Mass Distance is the Euclidean distance between the Center of Mass of the vesicle and the Center of Mass of its parent, which is a cell membrane, cytoplasm, nuclear membrane, or nucleus.

Type: Position, Per Time Point

Relative Center of Mass X Position is the difference between the x-coordinate of the vesicle’s Center of Mass and the x-coordinate of its parent’s Center of Mass. The vesicle’s parent (if it exists) is a cell membrane, cytoplasm, nuclear membrane, or nucleus.

Type: Position, Per Time Point

Relative Center of Mass Y Position is the difference between the y-coordinate of the vesicle’s Center of Mass and the y-coordinate of its parent’s Center of Mass. The vesicle’s parent (if it exists) is a cell membrane, cytoplasm, nuclear membrane, or nucleus.

Type: Position, Per Time Point

Relative Center of Mass Z Position is the difference between the z-coordinate of the vesicle’s Center of Mass and the z-coordinate of its parent’s Center of Mass. The vesicle’s parent (if it exists) is a cell membrane, cytoplasm, nuclear membrane, or nucleus.

Type: Position, Per Time Point

Relative Distance is the Euclidean distance between the Centroid of the vesicle and the Centroid of its parent, which is a cell membrane, cytoplasm, nuclear membrane, or nucleus.

Type: Position, Per Time Point

Relative X Position is the difference between the x-coordinate of the vesicle’s Centroid and the x-coordinate of its parent’s Centroid. The vesicle’s parent (if it exists) is a cell membrane, cytoplasm, nuclear membrane, or nucleus.

Type: Position, Per Time Point

Relative Y Position is the difference between the y-coordinate of the vesicle’s Centroid and the y-coordinate of its parent’s Centroid. The vesicle’s parent (if it exists) is a cell membrane, cytoplasm, nuclear membrane, or nucleus.

Type: Position, Per Time Point

Relative Z Position is the difference between the z-coordinate of the vesicle’s Centroid and the z-coordinate of its parent’s Centroid. The vesicle’s parent (if it exists) is a cell membrane, cytoplasm, nuclear membrane, or nucleus.

Cell

Type: Morphology, Per Time Point

The Area of the cell is equal to the Area of the cell membrane.

Type: Morphology, Per Time Point

Area to Contained Vesicle Area Ratio is the ratio of the Area of the cell to the sum of the Areas of all vesicles belonging to the cell.

Type: Morphology, Per Time Point

Bounding Depth is the depth (extent in Z) of the cell’s bounding box, which encloses the cell membrane.

Type: Morphology, Per Time Point

Bounding Height is the height (extent in Y) of the cell’s bounding box, which encloses the cell membrane.

Type: Morphology, Per Time Point

Bounding Width is the width (extent in X) of the cell’s bounding box, which encloses the cell membrane.

Type: Position, Per Time Point

Cell Center of Mass to Image Edge Distance is the distance from the Center of Mass of the cell to the nearest edge of the image.

Type: Position, Per Time Point

Cell Center to Image Edge Distance is the distance from the Centroid of the cell to the nearest edge of the image.

Type: Morphology, Per Time Point

Cell to Image Size Ratio is the ratio of the Area of the cell to the total image area.

Type: Morphology, Per Time Point

Cell/Cytoplasm Area Ratio is the ratio of the Area of the cell to the Area of the cytoplasm.

Type: Morphology, Per Time Point

Cell/Nucleus Area Ratio is the ratio of the Area of the cell to the Area of its nucleus.

Type: Morphology, Per Time Point

Cell/Organelle Area Ratio is the ratio of the Area of the cell to the sum of the Areas of all its vesicles and its nucleus.

Type: Position, Per Time Point

Center of Mass X is the x-coordinate of the cell’s Center of Mass. The Center of Mass is calculated as the average (mean) of the positions of all pixels contained by the cell-membrane outline.

Type: Position, Per Time Point

Center of Mass Y is the y-coordinate of the cell’s Center of Mass. The Center of Mass is calculated as the average (mean) of the positions of all pixels contained by the cell-membrane outline.

Type: Position, Per Time Point

Center to Nucleus Center Distance is the Euclidean distance between the Centroid of the cell and the Centroid of its nucleus.

Type: Position, Per Time Point

Centroid X is the x-coordinate of the center of the bounding box of the cell membrane.

Type: Position, Per Time Point

Centroid Y is the y-coordinate of the center of the bounding box of the cell membrane.

Type: Position, Per Time Point

Centroid Z is the z-coordinate of the center of the bounding box of the cell membrane.

Type: Count, Per Time Point

Contained Vesicle Count is the total number of vesicles assigned to the cell, meaning the total number of vesicles that are on the associated cell membrane, in the associated cytoplasm, on the associated nuclear membrane, or in the associated nucleus.

Type: Position, Per Time Point

Cytoplasm to Nucleus Vesicle Ratio is the ratio of the number of vesicles contained by the cell membrane or cytoplasm to the number of vesicles contained by the nuclear membrane or nucleus.

Type: Count, Per Time Point

Has Nucleus is a Boolean value that indicates whether the cell has a nucleus (1) or not (0).

Type: Morphology, Per Time Point

Max Contained Vesicle Area is the maximum of the Areas of all vesicles belonging to the cell.

Type: Position, Per Time Point

Max Contained Vesicle Distance to Center is the longest Euclidean distance between the Centroid of the cell and the Centroid of a vesicle belonging to the cell.

Type: Intensity, Per Time Point

Max Contained Vesicle Intensity is the maximum intensity of the given channel over all pixels contained by vesicles belonging to the cell. The image channel for the measurement is indicated in the measurement name; for example, the Max Contained Vesicle Intensity for a channel named “GFP” is called “Max Contained Vesicle Intensity (GFP)” or “Max Contained Vesicle Intensity - GFP.”

Type: Position, Per Time Point

Max Vesicle Center of Mass X is the maximum of the x-coordinates of the Centers of Mass of all vesicles in the cell.

Type: Position, Per Time Point

Max Vesicle Center of Mass Y is the maximum of the y-coordinates of the Centers of Mass of all vesicles in the cell.

Type: Morphology, Per Time Point

Mean Contained Vesicle Area is the mean of the Areas of all vesicles belonging to the cell.

Type: Position, Per Time Point

Mean Contained Vesicle Distance to Center is the mean Euclidean distance between the Centroid of the cell and the Centroid of a vesicle belonging to the cell.

Type: Intensity, Per Time Point

Mean Contained Vesicle Intensity is the mean of the Mean Intensities for the given channel for all vesicles belonging to the cell. The image channel for the measurement is indicated in the measurement name; for example, the Mean Contained Vesicle Intensity for a channel named “GFP” is called “Mean Contained Vesicle Intensity (GFP)” or “Mean Contained Vesicle Intensity - GFP.”

Type: Position, Per Time Point

Mean Vesicle Center of Mass X is the mean of the x-coordinates of the Centers of Mass of all vesicles in the cell.

Type: Position, Per Time Point

Mean Vesicle Center of Mass Y is the mean of the y-coordinates of the Centers of Mass of all vesicles in the cell.

Type: Position, Per Time Point

Min Cell Edge to Image Edge Distance is the shortest distance between a vertex of the cell membrane and an edge of the image.

Type: Morphology, Per Time Point

Min Contained Vesicle Area is the minimum of the Areas of all vesicles belonging to the cell.

Type: Position, Per Time Point

Min Contained Vesicle Distance to Center is the smallest Euclidean distance between the Centroid of the cell and the Centroid of a vesicle belonging to the cell.

Type: Intensity, Per Time Point

Min Contained Vesicle Intensity is the minimum intensity of the given channel over all pixels contained by vesicles belonging to the cell. The image channel for the measurement is indicated in the measurement name; for example, the Min Contained Vesicle Intensity for a channel named “GFP” is called “Min Contained Vesicle Intensity (GFP)” or “Min Contained Vesicle Intensity - GFP.”

Type: Position, Per Time Point

Min Edge to Nucleus Edge Distance is the shortest distance between a vertex of the cell membrane and a vertex of the associated nuclear membrane.

Type: Position, Per Time Point

Min Vesicle Center of Mass X is the minimum of the x-coordinates of the Centers of Mass of all vesicles in the cell.

Type: Position, Per Time Point

Min Vesicle Center of Mass Y is the minimum of the y-coordinates of the Centers of Mass of all vesicles in the cell.

Type: Morphology, Per Time Point

Bounding Depth is the depth (extent in Z) of the cell’s bounding box, which encloses the cell membrane.

Type: Morphology, Per Time Point

Bounding Height is the height (extent in Y) of the cell’s bounding box, which encloses the cell membrane.

Type: Morphology, Per Time Point

Bounding Width is the width (extent in X) of the cell’s bounding box, which encloses the cell membrane.

Type: Position, Per Time Point

Cell Center of Mass to Image Edge Distance is the distance from the Center of Mass of the cell to the nearest face of the image volume.

Type: Position, Per Time Point

Cell Center to Image Edge Distance is the distance from the Centroid of the cell to the nearest face of the image volume.

Type: Morphology, Per Time Point

Cell to Image Size Ratio is the ratio of the Volume of the cell to the total image volume.

Type: Morphology, Per Time Point

Cell/Cytoplasm Volume Ratio is the ratio of the Volume of the cell to the Volume of the cytoplasm.

Type: Morphology, Per Time Point

Cell/Nucleus Volume Ratio is the ratio of the Volume of the cell to the Volume of its nucleus.

Type: Morphology, Per Time Point

Cell/Organelle Volume Ratio is the ratio of the Volume of the cell to the sum of the Volumes of all its vesicles and its nucleus.

Type: Position, Per Time Point

Center of Mass X is the x-coordinate of the cell’s Center of Mass. The Center of Mass is calculated as the average (mean) of the positions of all voxels contained by the cell-membrane mesh.

Type: Position, Per Time Point

Center of Mass Y is the y-coordinate of the cell’s Center of Mass. The Center of Mass is calculated as the average (mean) of the positions of all voxels contained by the cell-membrane mesh.

Type: Position, Per Time Point

Center of Mass Z is the z-coordinate of the cell’s Center of Mass. The Center of Mass is calculated as the average (mean) of the positions of all voxels contained by the cell-membrane mesh.

Type: Position, Per Time Point

Center to Nucleus Center Distance is the Euclidean distance between the Centroid of the cell and the Centroid of its nucleus.

Type: Position, Per Time Point

Centroid X is the x-coordinate of the center of the bounding box of the cell membrane.

Type: Position, Per Time Point

Centroid Y is the y-coordinate of the center of the bounding box of the cell membrane.

Type: Position, Per Time Point

Centroid Z is the z-coordinate of the center of the bounding box of the cell membrane.

Type: Count, Per Time Point

Contained Vesicle Count is the total number of vesicles assigned to the cell, meaning the total number of vesicles that are on the associated cell membrane, in the associated cytoplasm, on the associated nuclear membrane, or in the associated nucleus.

Type: Position, Per Time Point

Cytoplasm to Nucleus Vesicle Ratio is the ratio of the number of vesicles contained by the cell membrane or cytoplasm to the number of vesicles contained by the nuclear membrane or nucleus.

Type: Count, Per Time Point

Has Nucleus is a Boolean value that indicates whether the cell has a nucleus (1) or not (0).

Type: Position, Per Time Point

Max Contained Vesicle Distance to Center is the longest Euclidean distance between the Centroid of the cell and the Centroid of a vesicle belonging to the cell.

Type: Intensity, Per Time Point

Max Contained Vesicle Intensity is the maximum intensity of the given channel over all voxels contained by vesicles belonging to the cell. The image channel for the measurement is indicated in the measurement name; for example, the Max Contained Vesicle Intensity for a channel named “GFP” is called “Max Contained Vesicle Intensity (GFP)” or “Max Contained Vesicle Intensity - GFP.”

Type: Morphology, Per Time Point

Max Contained Vesicle Volume is the maximum of the Volumes of all vesicles belonging to the cell.

Type: Position, Per Time Point

Max Vesicle Center of Mass X is the maximum of the x-coordinates of the Centers of Mass of all vesicles in the cell.

Type: Position, Per Time Point

Max Vesicle Center of Mass Y is the maximum of the y-coordinates of the Centers of Mass of all vesicles in the cell.

Type: Position, Per Time Point

Max Vesicle Center of Mass Z is the maximum of the z-coordinates of the Centers of Mass of all vesicles in the cell.

Type: Position, Per Time Point

Mean Contained Vesicle Distance to Center is the mean Euclidean distance between the Centroid of the cell and the Centroid of a vesicle belonging to the cell.

Type: Intensity, Per Time Point

Mean Contained Vesicle Intensity is the mean of the Mean Intensities for the given channel for all vesicles belonging to the cell. The image channel for the measurement is indicated in the measurement name; for example, the Mean Contained Vesicle Intensity for a channel named “GFP” is called “Mean Contained Vesicle Intensity (GFP)” or “Mean Contained Vesicle Intensity - GFP.”

Type: Morphology, Per Time Point

Mean Contained Vesicle Volume is the mean of the Volumes of all vesicles belonging to the cell.

Type: Position, Per Time Point

Mean Vesicle Center of Mass X is the mean of the x-coordinates of the Centers of Mass of all vesicles in the cell.

Type: Position, Per Time Point

Mean Vesicle Center of Mass Y is the mean of the y-coordinates of the Centers of Mass of all vesicles in the cell.

Type: Position, Per Time Point

Mean Vesicle Center of Mass Z is the mean of the z-coordinates of the Centers of Mass of all vesicles in the cell.

Type: Position, Per Time Point

Min Cell Edge to Image Edge Distance is the shortest distance between a vertex of the cell membrane and a face of the image volume. The lowest available level of detail of the cell-membrane mesh is used for this measurement calculation.

Type: Position, Per Time Point

Min Contained Vesicle Distance to Center is the smallest Euclidean distance between the Centroid of the cell and the Centroid of a vesicle belonging to the cell.

Type: Intensity, Per Time Point

Min Contained Vesicle Intensity is the minimum intensity of the given channel over all voxels contained by vesicles belonging to the cell. The image channel for the measurement is indicated in the measurement name; for example, the Min Contained Vesicle Intensity for a channel named “GFP” is called “Min Contained Vesicle Intensity (GFP)” or “Min Contained Vesicle Intensity - GFP.”

Type: Morphology, Per Time Point

Min Contained Vesicle Volume is the minimum of the Volumes of all vesicles belonging to the cell.

Type: Position, Per Time Point

Min Edge to Nucleus Edge Distance is the shortest distance between a vertex of the cell membrane and a vertex of the associated nuclear membrane. The lowest available level of detail of the cell-membrane and nuclear-membrane meshes is used for this measurement calculation.

Type: Position, Per Time Point

Min Vesicle Center of Mass X is the minimum of the x-coordinates of the Centers of Mass of all vesicles in the cell.

Type: Position, Per Time Point

Min Vesicle Center of Mass Y is the minimum of the y-coordinates of the Centers of Mass of all vesicles in the cell.

Type: Position, Per Time Point

Min Vesicle Center of Mass Z is the minimum of the z-coordinates of the Centers of Mass of all vesicles in the cell.

Type: Morphology, Per Time Point

The Volume of the cell is equal to the Volume of the cell membrane.

Type: Morphology, Per Time Point

Volume to Contained Vesicle Volume Ratio is the ratio of the Volume of the cell to the sum of the Volumes of all vesicles belonging to the cell.

Cytoplasm

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

Type: Morphology, Per Time Point

The Area of the cytoplasm is the difference of the Area of the cell and the Area of the nucleus, if it exists.

Type: Morphology, Per Time Point

Area to Contained Vesicle Area Ratio is the ratio of the Area of the cytoplasm to the sum of the Areas of all vesicles contained by the cytoplasm.

Type: Morphology, Per Time Point

Bounding Depth is the depth (extent in Z) of the cytoplasm’s bounding box.

Type: Morphology, Per Time Point

Bounding Height is the height (extent in Y) of the cytoplasm’s bounding box.

Type: Morphology, Per Time Point

Bounding Width is the width (extent in X) of the cytoplasm’s bounding box.

Type: Position, Per Time Point

Cell ID is the number of the cell object to which the cytoplasm is associated. Generally, the Cell ID is the same as the number in the cytoplasm name.

Type: Position, Per Time Point

Center of Mass X is the x-coordinate of the cytoplasm’s Center of Mass. The Center of Mass is calculated as the average (mean) of the positions of all pixels contained by the cytoplasm, meaning all pixels contained by the cell-membrane outline and excluded from the nuclear-membrane outline.

Type: Position, Per Time Point

Center of Mass Y is the y-coordinate of the cytoplasm’s Center of Mass. The Center of Mass is calculated as the average (mean) of the positions of all pixels contained by the cytoplasm, meaning all pixels contained by the cell-membrane outline and excluded from the nuclear-membrane outline.

Type: Position, Per Time Point

Centroid X is the x-coordinate of the center of the cytoplasm’s bounding box.

Type: Position, Per Time Point

Centroid Y is the y-coordinate of the center of the cytoplasm’s bounding box.

Type: Position, Per Time Point

Centroid Z is the z-coordinate of the center of the cytoplasm’s bounding box.

Type: Count, Per Time Point

Contained Vesicle Count is the total number of vesicles in the cytoplasm.

Type: Morphology, Per Time Point

Cytoplasm to Image Size Ratio is the ratio of the Area of the cytoplasm to the total image area.

Type: Morphology, Per Time Point

Max Contained Vesicle Area is the maximum of the Areas of all vesicles in the cytoplasm.

Type: Position, Per Time Point

Max Contained Vesicle Distance to Center is the longest distance between the Centroid of a vesicle in the cytoplasm and the Centroid of the cytoplasm.

Type: Intensity, Per Time Point

Max Contained Vesicle Intensity is the maximum intensity of the given channel over all pixels contained by vesicles that are contained by the cytoplasm. The image channel for the measurement is indicated in the measurement name; for example, the Max Contained Vesicle Intensity for a channel named “GFP” is called “Max Contained Vesicle Intensity (GFP)” or “Max Contained Vesicle Intensity - GFP.”

Type: Intensity, Per Time Point

Max Intensity is the maximum intensity for the given channel over all pixels contained by the cytoplasm. The image channel for the measurement is indicated in the measurement name; for example, the Max Intensity for a channel named “GFP” is called “Max Intensity (GFP)” or “Max Intensity - GFP.” This measurement is only valid when the nucleus is completely contained by the cell membrane or when there is no detected nucleus.

Type: Position, Per Time Point

Max Vesicle Center of Mass X is the maximum of the x-coordinates of the Centers of Mass of all vesicles in the cytoplasm.

Type: Position, Per Time Point

Max Vesicle Center of Mass Y is the maximum of the y-coordinates of the Centers of Mass of all vesicles in the cytoplasm.

Type: Morphology, Per Time Point

Max Vesicle Distance to Nuclear Membrane Edge is the maximum distance from the Center of Mass of a vesicle in the cell to the respective closest vertex on the edge of the nuclear membrane.

Type: Morphology, Per Time Point

Mean Contained Vesicle Area is the mean of the Areas of all vesicles in the cytoplasm.

Type: Position, Per Time Point

Mean Contained Vesicle Distance to Center is the mean distance between the Centroid of a vesicle in the cytoplasm and the Centroid of the cytoplasm.

Type: Intensity, Per Time Point

Mean Contained Vesicle Intensity is the mean of the Mean Intensities for the given channel for all vesicles contained by the cytoplasm. The image channel for the measurement is indicated in the measurement name; for example, the Mean Contained Vesicle Intensity for a channel named “GFP” is called “Mean Contained Vesicle Intensity (GFP)” or “Mean Contained Vesicle Intensity - GFP.”

Type: Intensity, Per Time Point

Mean Intensity is the mean intensity for the given channel over all pixels contained by the cytoplasm. The image channel for the measurement is indicated in the measurement name; for example, the Mean Intensity for a channel named “GFP” is called “Mean Intensity (GFP)” or “Mean Intensity - GFP.” This measurement is only valid when the nucleus is completely contained by the cell membrane or when there is no detected nucleus.

Type: Position, Per Time Point

Mean Vesicle Center of Mass X is the mean of the x-coordinates of the Centers of Mass of all vesicles in the cytoplasm.

Type: Position, Per Time Point

Mean Vesicle Center of Mass Y is the mean of the y-coordinates of the Centers of Mass of all vesicles in the cytoplasm.

Type: Morphology, Per Time Point

Mean Vesicle Distance to Nuclear Membrane Edge is the mean distance from the Center of Mass of a vesicle in the cell to the respective closest vertex on the edge of the nuclear membrane.

Type: Morphology, Per Time Point

Min Contained Vesicle Area is the minimum of the Areas of all vesicles in the cytoplasm.

Type: Position, Per Time Point

Min Contained Vesicle Distance to Center is the shortest distance between the Centroid of a vesicle in the cytoplasm and the Centroid of the cytoplasm.

Type: Intensity, Per Time Point

Min Contained Vesicle Intensity is the minimum intensity of the given channel over all pixels contained by vesicles that are contained by the cytoplasm. The image channel for the measurement is indicated in the measurement name; for example, the Min Contained Vesicle Intensity for a channel named “GFP” is called “Min Contained Vesicle Intensity (GFP)” or “Min Contained Vesicle Intensity - GFP.”

Type: Intensity, Per Time Point

Min Intensity is the minimum intensity for the given channel over all pixels contained by the cytoplasm. The image channel for the measurement is indicated in the measurement name; for example, the Min Intensity for a channel named “GFP” is called “Min Intensity (GFP)” or “Min Intensity - GFP.” This measurement is only valid when the nucleus is completely contained by the cell membrane or when there is no detected nucleus.

Type: Position, Per Time Point

Min Vesicle Center of Mass X is the minimum of the x-coordinates of the Centers of Mass of all vesicles in the cytoplasm.

Type: Position, Per Time Point

Min Vesicle Center of Mass Y is the minimum of the y-coordinates of the Centers of Mass of all vesicles in the cytoplasm.

Type: Morphology, Per Time Point

Min Vesicle Distance to Nuclear Membrane Edge is the minimum distance from the Center of Mass of a vesicle in the cell to the respective closest vertex on the edge of the nuclear membrane.

Type: Intensity, Per Time Point

Std. Dev. Intensity is the standard deviation of the intensity for the given channel over all pixels contained by the cytoplasm. The image channel for the measurement is indicated in the measurement name; for example, the Std. Dev. Intensity for a channel named “GFP” is called “Std. Dev. Intensity (GFP)” or “Std. Dev. Intensity - GFP.” This measurement is only valid when the nucleus is completely contained by the cell membrane or when there is no detected nucleus.

Type: Intensity, Per Time Point

Total Intensity is the sum of the intensities for the given channel over all pixels contained by the cytoplasm. The image channel for the measurement is indicated in the measurement name; for example, the Total Intensity for a channel named “GFP” is called “Total Intensity (GFP)” or “Total Intensity - GFP.” This measurement is only valid when the nucleus is completely contained by the cell membrane or when there is no detected nucleus.

Type: Morphology, Per Time Point

Bounding Depth is the depth (extent in Z) of the cytoplasm’s bounding box.

Type: Morphology, Per Time Point

Bounding Height is the height (extent in Y) of the cytoplasm’s bounding box.

Type: Morphology, Per Time Point

Bounding Width is the width (extent in X) of the cytoplasm’s bounding box.

Type: Position, Per Time Point

Cell ID is the number of the cell object to which the cytoplasm is associated. Generally, the Cell ID is the same as the number in the cytoplasm name.

Type: Position, Per Time Point

Center of Mass X is the x-coordinate of the cytoplasm’s Center of Mass. The Center of Mass is calculated as the average (mean) of the positions of all voxels contained by the cytoplasm, meaning all voxels contained by the cell-membrane mesh and excluded from the nuclear-membrane mesh.

Type: Position, Per Time Point

Center of Mass Y is the y-coordinate of the cytoplasm’s Center of Mass. The Center of Mass is calculated as the average (mean) of the positions of all voxels contained by the cytoplasm, meaning all voxels contained by the cell-membrane mesh and excluded from the nuclear-membrane mesh.

Type: Position, Per Time Point

Center of Mass Z is the z-coordinate of the cytoplasm’s Center of Mass. The Center of Mass is calculated as the average (mean) of the positions of all voxels contained by the cytoplasm, meaning all voxels contained by the cell-membrane mesh and excluded from the nuclear-membrane mesh.

Type: Position, Per Time Point

Centroid X is the x-coordinate of the center of the cytoplasm’s bounding box.

Type: Position, Per Time Point

Centroid Y is the y-coordinate of the center of the cytoplasm’s bounding box.

Type: Position, Per Time Point

Centroid Z is the z-coordinate of the center of the cytoplasm’s bounding box.

Type: Count, Per Time Point

Contained Vesicle Count is the total number of vesicles in the cytoplasm.

Type: Morphology, Per Time Point

Cytoplasm to Image Size Ratio is the ratio of the Volume of the cytoplasm to the total image volume.

Type: Position, Per Time Point

Max Contained Vesicle Distance to Center is the longest distance between the Centroid of a vesicle in the cytoplasm and the Centroid of the cytoplasm.

Type: Intensity, Per Time Point

Max Contained Vesicle Intensity is the maximum intensity of the given channel over all voxels contained by vesicles that are contained by the cytoplasm. The image channel for the measurement is indicated in the measurement name; for example, the Max Contained Vesicle Intensity for a channel named “GFP” is called “Max Contained Vesicle Intensity (GFP)” or “Max Contained Vesicle Intensity - GFP.”

Type: Morphology, Per Time Point

Max Contained Vesicle Volume is the maximum of the Volumes of all vesicles in the cytoplasm.

Type: Intensity, Per Time Point

Max Intensity is the maximum intensity for the given channel over all voxels contained by the cytoplasm, which is equivalent to all voxels contained by the cell membrane but not the nuclear membrane. The image channel for the measurement is indicated in the measurement name; for example, the Max Intensity for a channel named “GFP” is called “Max Intensity (GFP)” or “Max Intensity - GFP.”

Type: Position, Per Time Point

Max Vesicle Center of Mass X is the maximum of the x-coordinates of the Centers of Mass of all vesicles in the cytoplasm.

Type: Position, Per Time Point

Max Vesicle Center of Mass Y is the maximum of the y-coordinates of the Centers of Mass of all vesicles in the cytoplasm.

Type: Position, Per Time Point

Max Vesicle Center of Mass Z is the maximum of the z-coordinates of the Centers of Mass of all vesicles in the cytoplasm.

Type: Morphology, Per Time Point

Max Vesicle Distance to Nuclear Membrane Edge is the maximum distance from the Center of Mass of a vesicle in the cell to the respective closest point on the edge of the nuclear membrane.

Type: Position, Per Time Point

Mean Contained Vesicle Distance to Center is the mean distance between the Centroid of a vesicle in the cytoplasm and the Centroid of the cytoplasm.

Type: Intensity, Per Time Point

Mean Contained Vesicle Intensity is the mean of the Mean Intensities for the given channel for all vesicles contained by the cytoplasm. The image channel for the measurement is indicated in the measurement name; for example, the Mean Contained Vesicle Intensity for a channel named “GFP” is called “Mean Contained Vesicle Intensity (GFP)” or “Mean Contained Vesicle Intensity - GFP.”

Type: Morphology, Per Time Point

Mean Contained Vesicle Volume is the mean of the Volumes of all vesicles in the cytoplasm.

Type: Intensity, Per Time Point

Mean Intensity is the mean intensity for the given channel over all voxels contained by the cytoplasm, which is equivalent to all voxels contained by the cell membrane but not the nuclear membrane. The image channel for the measurement is indicated in the measurement name; for example, the Mean Intensity for a channel named “GFP” is called “Mean Intensity (GFP)” or “Mean Intensity - GFP.”

Type: Position, Per Time Point

Mean Vesicle Center of Mass X is the mean of the x-coordinates of the Centers of Mass of all vesicles in the cytoplasm.

Type: Position, Per Time Point

Mean Vesicle Center of Mass Y is the mean of the y-coordinates of the Centers of Mass of all vesicles in the cytoplasm.

Type: Position, Per Time Point

Mean Vesicle Center of Mass Z is the mean of the z-coordinates of the Centers of Mass of all vesicles in the cytoplasm.

Type: Morphology, Per Time Point

Mean Vesicle Distance to Nuclear Membrane Edge is the mean distance from the Center of Mass of a vesicle in the cell to the respective closest point on the edge of the nuclear membrane.

Type: Position, Per Time Point

Min Contained Vesicle Distance to Center is the shortest distance between the Centroid of a vesicle in the cytoplasm and the Centroid of the cytoplasm.

Type: Intensity, Per Time Point

Min Contained Vesicle Intensity is the minimum intensity of the given channel over all voxels contained by vesicles that are contained by the cytoplasm. The image channel for the measurement is indicated in the measurement name; for example, the Min Contained Vesicle Intensity for a channel named “GFP” is called “Min Contained Vesicle Intensity (GFP)” or “Min Contained Vesicle Intensity - GFP.”

Type: Morphology, Per Time Point

Min Contained Vesicle Volume is the minimum of the Volumes of all vesicles in the cytoplasm.

Type: Intensity, Per Time Point

Min Intensity is the minimum intensity for the given channel over all voxels contained by the cytoplasm, which is equivalent to all voxels contained by the cell membrane but not the nuclear membrane. The image channel for the measurement is indicated in the measurement name; for example, the Min Intensity for a channel named “GFP” is called “Min Intensity (GFP)” or “Min Intensity - GFP.”

Type: Position, Per Time Point

Min Vesicle Center of Mass X is the minimum of the x-coordinates of the Centers of Mass of all vesicles in the cytoplasm.

Type: Position, Per Time Point

Min Vesicle Center of Mass Y is the minimum of the y-coordinates of the Centers of Mass of all vesicles in the cytoplasm.

Type: Position, Per Time Point

Min Vesicle Center of Mass Z is the minimum of the z-coordinates of the Centers of Mass of all vesicles in the cytoplasm.

Type: Morphology, Per Time Point

Min Vesicle Distance to Nuclear Membrane Edge is the minimum distance from the Center of Mass of a vesicle in the cell to the respective closest point on the edge of the nuclear membrane.

Type: Intensity, Per Time Point

Std. Dev. Intensity is the standard deviation of the intensity for the given channel over all voxels contained by the cytoplasm, which is equivalent to all voxels contained by the cell membrane but not the nuclear membrane. The image channel for the measurement is indicated in the measurement name; for example, the Std. Dev. Intensity for a channel named “GFP” is called “Std. Dev. Intensity (GFP)” or “Std. Dev. Intensity - GFP.”

Type: Intensity, Per Time Point

Total Intensity is the sum of the intensities for the given channel over all voxels contained by the cytoplasm, which is equivalent to all voxels contained by the cell membrane but not the nuclear membrane. The image channel for the measurement is indicated in the measurement name; for example, the Total Intensity for a channel named “GFP” is called “Total Intensity (GFP)” or “Total Intensity - GFP.”

Type: Morphology, Per Time Point

The Volume of the cytoplasm is the difference of the Volume of the cell and the Volume of the nucleus, if it exists.

Type: Morphology, Per Time Point

Volume to Contained Vesicle Volume Ratio is the ratio of the Volume of the cytoplasm to the sum of the Volumes of all vesicles contained by the cytoplasm.

Nucleus

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

Type: Morphology, Per Time Point

% Overlapped is the percentage of the nucleus area that is overlapped with its parent cell.

Type: Morphology, Per Time Point

The Area of the nucleus is equal to the Area of the nuclear membrane.

Type: Morphology, Per Time Point

Area Overlapped is the area of the nucleus that is overlapped with its parent cell.

Type: Morphology, Per Time Point

Area to Contained Vesicle Area Ratio is the ratio of the Area of the nucleus to the sum of the Areas of all vesicles contained by the nucleus.

Type: Morphology, Per Time Point

Bounding Depth is the depth (extent in Z) of the nucleus’ bounding box.

Type: Morphology, Per Time Point

Bounding Height is the height (extent in Y) of the nucleus' bounding box.

Type: Morphology, Per Time Point

Bounding Width is the width (extent in X) of the nucleus' bounding box.

Type: Position, Per Time Point

Cell ID is the number of the cell object to which the nucleus is associated. Generally, the Cell ID is the same as the number in the nucleus name.

Type: Position, Per Time Point

Center of Mass X is the x-coordinate of the nucleus' Center of Mass. The Center of Mass is calculated as the average (mean) of the positions of all pixels contained by the nucleus.

Type: Position, Per Time Point

Center of Mass Y is the y-coordinate of the nucleus' Center of Mass. The Center of Mass is calculated as the average (mean) of the positions of all pixels contained by the nucleus.

Type: Position, Per Time Point

Centroid X is the x-coordinate of the center of the nucleus' bounding box.

Type: Position, Per Time Point

Centroid Y is the y-coordinate of the center of the nucleus' bounding box.

Type: Position, Per Time Point

Centroid Z is the z-coordinate of the center of the nucleus' bounding box.

Type: Count, Per Time Point

Contained Vesicle Count is the total number of vesicles in the nucleus.

Type: Morphology, Per Time Point

Max Contained Vesicle Area is the maximum of the Areas of all vesicles in the nucleus.

Type: Position, Per Time Point

Max Contained Vesicle Distance to Center is the longest distance between the Centroid of a vesicle in the nucleus and the Centroid of the nucleus.

Type: Intensity, Per Time Point

Max Contained Vesicle Intensity is the maximum intensity of the given channel over all pixels contained by vesicles that are in the nucleus. The image channel for the measurement is indicated in the measurement name; for example, the Max Contained Vesicle Intensity for a channel named “GFP” is called “Max Contained Vesicle Intensity (GFP)” or “Max Contained Vesicle Intensity - GFP.”

Type: Intensity, Per Time Point

Max Intensity is the maximum intensity for the given channel over all pixels contained by the nucleus. The image channel for the measurement is indicated in the measurement name; for example, the Max Intensity for a channel named “GFP” is called “Max Intensity (GFP)” or “Max Intensity - GFP.”

Type: Position, Per Time Point

Max Vesicle Center of Mass X is the maximum of the x-coordinates of the Centers of Mass of all vesicles in the nucleus.

Type: Position, Per Time Point

Max Vesicle Center of Mass Y is the maximum of the y-coordinates of the Centers of Mass of all vesicles in the nucleus.

Type: Morphology, Per Time Point

Mean Contained Vesicle Area is the mean of the Areas of all vesicles in the nucleus.

Type: Position, Per Time Point

Mean Contained Vesicle Distance to Center is the mean distance between the Centroid of a vesicle in the nucleus and the Centroid of the nucleus.

Type: Intensity, Per Time Point

Mean Contained Vesicle Intensity is the mean of the Mean Intensities for the given channel for all vesicles in the nucleus. The image channel for the measurement is indicated in the measurement name; for example, the Mean Contained Vesicle Intensity for a channel named “GFP” is called “Mean Contained Vesicle Intensity (GFP)” or “Mean Contained Vesicle Intensity - GFP.”

Type: Intensity, Per Time Point

Mean Intensity is the mean intensity for the given channel over all pixels contained by the nucleus. The image channel for the measurement is indicated in the measurement name; for example, the Mean Intensity for a channel named “GFP” is called “Mean Intensity (GFP)” or “Mean Intensity - GFP.”

Type: Position, Per Time Point

Mean Vesicle Center of Mass X is the mean of the x-coordinates of the Centers of Mass of all vesicles in the nucleus.

Type: Position, Per Time Point

Mean Vesicle Center of Mass Y is the mean of the y-coordinates of the Centers of Mass of all vesicles in the nucleus.

Type: Position, Per Time Point

Min Center of Mass to Cell Edge Distance is the shortest Euclidean distance between the Center of Mass of the nucleus and a vertex of the cell membrane.

Type: Morphology, Per Time Point

Min Contained Vesicle Area is the minimum of the Areas of all vesicles contained by the nucleus.

Type: Position, Per Time Point

Min Contained Vesicle Distance to Center is the shortest distance between the Centroid of a vesicle in the nucleus and the Centroid of the nucleus.

Type: Intensity, Per Time Point

Min Contained Vesicle Intensity is the minimum intensity of the given channel over all pixels contained by vesicles that are contained by the nucleus. The image channel for the measurement is indicated in the measurement name; for example, the Min Contained Vesicle Intensity for a channel named “GFP” is called “Min Contained Vesicle Intensity (GFP)” or “Min Contained Vesicle Intensity - GFP.”

Type: Intensity, Per Time Point

Min Intensity is the minimum intensity for the given channel over all pixels contained by the nucleus. The image channel for the measurement is indicated in the measurement name; for example, the Min Intensity for a channel named “GFP” is called “Min Intensity (GFP)” or “Min Intensity - GFP.”

Type: Position, Per Time Point

Min Vesicle Center of Mass X is the minimum of the x-coordinates of the Centers of Mass of all vesicles in the nucleus.

Type: Position, Per Time Point

Min Vesicle Center of Mass Y is the minimum of the y-coordinates of the Centers of Mass of all vesicles in the nucleus.

Type: Morphology, Per Time Point

Nucleus to Image Size Ratio is the ratio of the Area of the nucleus to the total image area.

Type: Count, Per Time Point

Relations on Frame for nuclei is the sum of the Contained Vesicle Count for the nucleus and the number of related cells (always 1).

Type: Position, Per Time Point

Relative Center of Mass Distance is the Euclidean distance from the Center of Mass of the nucleus to the Center of Mass of its parent cell.

Type: Position, Per Time Point

Relative Center of Mass X Position is the difference between the x-coordinate of the nucleus' Center of Mass and the x-coordinate of its parent cell’s Center of Mass.

Type: Position, Per Time Point

Relative Center of Mass Y Position is the difference between the y-coordinate of the nucleus' Center of Mass and the y-coordinate of its parent cell’s Center of Mass.

Type: Position, Per Time Point

Relative Center of Mass Z Position is the difference between the z-coordinate of the nucleus' Center of Mass and the z-coordinate of its parent cell’s Center of Mass.

Type: Position, Per Time Point

Relative Distance is the Euclidean distance from the Centroid of the nucleus to the Centroid of its parent cell.

Type: Position, Per Time Point

Relative X Position is the difference between the x-coordinate of the nucleus' Centroid and the x-coordinate of its parent cell’s Centroid.

Type: Position, Per Time Point

Relative Y Position is the difference between the y-coordinate of the nucleus' Centroid and the y-coordinate of its parent cell’s Centroid.

Type: Intensity, Per Time Point

Std Dev Intensity is the standard deviation of the intensity for the given channel over all pixels contained by the nucleus. The image channel for the measurement is indicated in the measurement name; for example, the Std Dev Intensity for a channel named “GFP” is called “Std Dev Intensity (GFP)” or “Std Dev Intensity - GFP.”

Type: Intensity, Per Time Point

Total Intensity is the sum of the intensities for the given channel over all pixels contained by the nucleus. The image channel for the measurement is indicated in the measurement name; for example, the Total Intensity for a channel named “GFP” is called “Total Intensity (GFP)” or “Total Intensity - GFP.”

Type: Morphology, Per Time Point

Bounding Depth is the depth (extent in Z) of the nucleus’ bounding box.

Type: Morphology, Per Time Point

Bounding Height is the height (extent in Y) of the nucleus' bounding box.

Type: Morphology, Per Time Point

Bounding Width is the width (extent in X) of the nucleus' bounding box.

Type: Position, Per Time Point

Cell ID is the number of the cell object to which the nucleus is associated. Generally, the Cell ID is the same as the number in the nucleus name.

Type: Position, Per Time Point

Center of Mass X is the x-coordinate of the nucleus' Center of Mass. The Center of Mass is calculated as the average (mean) of the positions of all voxels contained by the nucleus.

Type: Position, Per Time Point

Center of Mass Y is the y-coordinate of the nucleus' Center of Mass. The Center of Mass is calculated as the average (mean) of the positions of all voxels contained by the nucleus.

Type: Position, Per Time Point

Center of Mass Z is the z-coordinate of the nucleus' Center of Mass. The Center of Mass is calculated as the average (mean) of the positions of all voxels contained by the nucleus.

Type: Position, Per Time Point

Centroid X is the x-coordinate of the center of the nucleus' bounding box.

Type: Position, Per Time Point

Centroid Y is the y-coordinate of the center of the nucleus' bounding box.

Type: Position, Per Time Point

Centroid Z is the z-coordinate of the center of the nucleus' bounding box.

Type: Count, Per Time Point

Contained Vesicle Count is the total number of vesicles in the nucleus.

Type: Position, Per Time Point

Max Contained Vesicle Distance to Center is the longest distance between the Centroid of a vesicle in the nucleus and the Centroid of the nucleus.

Type: Intensity, Per Time Point

Max Contained Vesicle Intensity is the maximum intensity of the given channel over all voxels contained by vesicles that are in the nucleus. The image channel for the measurement is indicated in the measurement name; for example, the Max Contained Vesicle Intensity for a channel named “GFP” is called “Max Contained Vesicle Intensity (GFP)” or “Max Contained Vesicle Intensity - GFP.”

Type: Morphology, Per Time Point

Max Contained Vesicle Volume is the maximum of the Volumes of all vesicles in the nucleus.

Type: Intensity, Per Time Point

Max Intensity is the maximum intensity for the given channel over all voxels contained by the nucleus. The image channel for the measurement is indicated in the measurement name; for example, the Max Intensity for a channel named “GFP” is called “Max Intensity (GFP)” or “Max Intensity - GFP.”

Type: Position, Per Time Point

Max Vesicle Center of Mass X is the maximum of the x-coordinates of the Centers of Mass of all vesicles in the nucleus.

Type: Position, Per Time Point

Max Vesicle Center of Mass Y is the maximum of the y-coordinates of the Centers of Mass of all vesicles in the nucleus.

Type: Position, Per Time Point

Max Vesicle Center of Mass Z is the maximum of the z-coordinates of the Centers of Mass of all vesicles in the nucleus.

Type: Position, Per Time Point

Mean Contained Vesicle Distance to Center is the mean distance between the Centroid of a vesicle in the nucleus and the Centroid of the nucleus.

Type: Intensity, Per Time Point

Mean Contained Vesicle Intensity is the mean of the Mean Intensities for the given channel for all vesicles in the nucleus. The image channel for the measurement is indicated in the measurement name; for example, the Mean Contained Vesicle Intensity for a channel named “GFP” is called “Mean Contained Vesicle Intensity (GFP)” or “Mean Contained Vesicle Intensity - GFP.”

Type: Morphology, Per Time Point

Mean Contained Vesicle Volume is the mean of the Volumes of all vesicles in the nucleus.

Type: Intensity, Per Time Point

Mean Intensity is the mean intensity for the given channel over all voxels contained by the nucleus. The image channel for the measurement is indicated in the measurement name; for example, the Mean Intensity for a channel named “GFP” is called “Mean Intensity (GFP)” or “Mean Intensity - GFP.”

Type: Position, Per Time Point

Mean Vesicle Center of Mass X is the mean of the x-coordinates of the Centers of Mass of all vesicles in the nucleus.

Type: Position, Per Time Point

Mean Vesicle Center of Mass Y is the mean of the y-coordinates of the Centers of Mass of all vesicles in the nucleus.

Type: Position, Per Time Point

Mean Vesicle Center of Mass Z is the mean of the z-coordinates of the Centers of Mass of all vesicles in the nucleus.

Type: Position, Per Time Point

Min Center of Mass to Cell Edge Distance is the shortest Euclidean distance between the Center of Mass of the nucleus and a vertex of the cell membrane. The lowest available level of detail of the cell-membrane mesh is used for this measurement calculation.

Type: Position, Per Time Point

Min Contained Vesicle Distance to Center is the shortest distance between the Centroid of a vesicle in the nucleus and the Centroid of the nucleus.

Type: Intensity, Per Time Point

Min Contained Vesicle Intensity is the minimum intensity of the given channel over all voxels contained by vesicles that are contained by the nucleus. The image channel for the measurement is indicated in the measurement name; for example, the Min Contained Vesicle Intensity for a channel named “GFP” is called “Min Contained Vesicle Intensity (GFP)” or “Min Contained Vesicle Intensity - GFP.”

Type: Morphology, Per Time Point

Min Contained Vesicle Volume is the minimum of the Volumes of all vesicles contained by the nucleus.

Type: Intensity, Per Time Point

Min Intensity is the minimum intensity for the given channel over all voxels contained by the nucleus. The image channel for the measurement is indicated in the measurement name; for example, the Min Intensity for a channel named “GFP” is called “Min Intensity (GFP)” or “Min Intensity - GFP.”

Type: Position, Per Time Point

Min Vesicle Center of Mass X is the minimum of the x-coordinates of the Centers of Mass of all vesicles in the nucleus.

Type: Position, Per Time Point

Min Vesicle Center of Mass Y is the minimum of the y-coordinates of the Centers of Mass of all vesicles in the nucleus.

Type: Position, Per Time Point

Min Vesicle Center of Mass Z is the minimum of the z-coordinates of the Centers of Mass of all vesicles in the nucleus.

Type: Morphology, Per Time Point

Nucleus to Image Size Ratio is the ratio of the Volume of the nucleus to the total image volume.

Type: Count, Per Time Point

Relations on Frame for nuclei is the sum of the Contained Vesicle Count for the nucleus and the number of related cells (always 1).

Type: Position, Per Time Point

Relative Center of Mass Distance is the Euclidean distance from the Center of Mass of the nucleus to the Center of Mass of its parent cell.

Type: Position, Per Time Point

Relative Center of Mass X Position is the difference between the x-coordinate of the nucleus' Center of Mass and the x-coordinate of its parent cell’s Center of Mass.

Type: Position, Per Time Point

Relative Center of Mass Y Position is the difference between the y-coordinate of the nucleus' Center of Mass and the y-coordinate of its parent cell’s Center of Mass.

Type: Position, Per Time Point

Relative Center of Mass Z Position is the difference between the z-coordinate of the nucleus' Center of Mass and the z-coordinate of its parent cell’s Center of Mass.

Type: Position, Per Time Point

Relative Distance is the Euclidean distance from the Centroid of the nucleus to the Centroid of its parent cell.

Type: Position, Per Time Point

Relative X Position is the difference between the x-coordinate of the nucleus' Centroid and the x-coordinate of its parent cell’s Centroid.

Type: Position, Per Time Point

Relative Y Position is the difference between the y-coordinate of the nucleus' Centroid and the y-coordinate of its parent cell’s Centroid.

Type: Position, Per Time Point

Relative Z Position is the difference between the z-coordinate of the nucleus' Centroid and the z-coordinate of its parent cell’s Centroid.

Type: Intensity, Per Time Point

Std Dev Intensity is the standard deviation of the intensity for the given channel over all voxels contained by the nucleus. The image channel for the measurement is indicated in the measurement name; for example, the Std Dev Intensity for a channel named “GFP” is called “Std Dev Intensity (GFP)” or “Std Dev Intensity - GFP.”

Type: Intensity, Per Time Point

Total Intensity is the sum of the intensities for the given channel over all voxels contained by the nucleus. The image channel for the measurement is indicated in the measurement name; for example, the Total Intensity for a channel named “GFP” is called “Total Intensity (GFP)” or “Total Intensity - GFP.”

Type: Morphology, Per Time Point

The Volume of the nucleus is equal to the Volume of the nuclear membrane.

Type: Morphology, Per Time Point

Volume to Contained Vesicle Volume Ratio is the ratio of the Volume of the nucleus to the sum of the Volumes of all vesicles contained by the nucleus.

Relation

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

Type: Morphology, Per Time Point

% Overlapped is the percentage of the object that is overlapped with any related objects in the secondary/associate set(s).

Type: Morphology, Per Time Point

Area Overlapped is the area of the object that is overlapped with any related objects in the secondary/associate set(s).

Type: Position, Per Time Point

Minimum Relative Distance is the minimum of the Relative Distance measurements for all relations where the object is the primary object in the relation on the current time frame.

Type: Count, Per Time Point

Relations on Frame is the number of relations in which the object is the primary object in the relation on the current time frame.

Type: Position, Per Time Point

Relative Center of Mass Distance is the Euclidean distance between the Center of Mass of the object and the Center of Mass of the related, primary object. Relative Center of Mass Distance is calculated for objects in the secondary/associate sets of relations.

Type: Position, Per Time Point

Relative Center of Mass X Position is the x-coordinate of the Center of Mass of the object when the origin is considered to be the Center of Mass of the related, primary object. Relative Center of Mass X Position is calculated for objects in the secondary/associate sets of relations.

Type: Position, Per Time Point

Relative Center of Mass Y Position is the y-coordinate of the Center of Mass of the object when the origin is considered to be the Center of Mass of the related, primary object. Relative Center of Mass Y Position is calculated for objects in the secondary/associate sets of relations.

Type: Position, Per Time Point

Relative Center of Mass Z Position is the z-coordinate of the Center of Mass of the object when the origin is considered to be the Center of Mass of the related, primary object. Relative Center of Mass Z Position is calculated for objects in the secondary/associate sets of relations.

Type: Position, Per Time Point

Relative Distance is the Euclidean distance between the Centroid of the object and the Centroid of the related, primary object. Relative Distance is calculated for objects in the secondary/associate sets of relations.

Type: Position, Per Time Point

Relative X Position is the x-coordinate of the Centroid of the object when the origin is considered to be the Centroid of the related, primary object. Relative X Position is calculated for objects in the secondary/associate sets of relations.

Type: Position, Per Time Point

Relative Y Position is the y-coordinate of the Centroid of the object when the origin is considered to be the Centroid of the related, primary object. Relative Y Position is calculated for objects in the secondary/associate sets of relations.

Type: Position, Per Time Point

Minimum Relative Distance is the minimum of the Relative Distance measurements for all relations where the object is the primary object in the relation on the current time frame.

Type: Count, Per Time Point

Relations on Frame is the number of relations in which the object is the primary object in the relation on the current time frame.

Type: Position, Per Time Point

Relative Center of Mass Distance is the Euclidean distance between the Center of Mass of the object and the Center of Mass of the related, primary object. Relative Center of Mass Distance is calculated for objects in the secondary/associate sets of relations.

Type: Position, Per Time Point

Relative Center of Mass X Position is the x-coordinate of the Center of Mass of the object when the origin is considered to be the Center of Mass of the related, primary object. Relative Center of Mass X Position is calculated for objects in the secondary/associate sets of relations.

Type: Position, Per Time Point

Relative Center of Mass Y Position is the y-coordinate of the Center of Mass of the object when the origin is considered to be the Center of Mass of the related, primary object. Relative Center of Mass Y Position is calculated for objects in the secondary/associate sets of relations.

Type: Position, Per Time Point

Relative Center of Mass Z Position is the z-coordinate of the Center of Mass of the object when the origin is considered to be the Center of Mass of the related, primary object. Relative Center of Mass Z Position is calculated for objects in the secondary/associate sets of relations.

Type: Position, Per Time Point

Relative Distance is the Euclidean distance between the Centroid of the object and the Centroid of the related, primary object. Relative Distance is calculated for objects in the secondary/associate sets of relations.

Type: Position, Per Time Point

Relative X Position is the x-coordinate of the Centroid of the object when the origin is considered to be the Centroid of the related, primary object. Relative X Position is calculated for objects in the secondary/associate sets of relations.

Type: Position, Per Time Point

Relative Y Position is the y-coordinate of the Centroid of the object when the origin is considered to be the Centroid of the related, primary object. Relative Y Position is calculated for objects in the secondary/associate sets of relations.

Type: Position, Per Time Point

Relative Z Position is the z-coordinate of the Centroid of the object when the origin is considered to be the Centroid of the related, primary object. Relative Z Position is calculated for objects in the secondary/associate sets of relations.

Track relation

Type: Count, Over All Time

All Relations Count is the total number of relations involving the object across all time frames and is equal to the sum of Relation Primary Count and Relation Secondary Count.

Type: Position, Over All Time

First Relation Frame is the earliest frame on which the object is related to another object. The first frame of the dataset is considered frame zero (0).

Type: Count, Over All Time

Has Relation is one (1) if the object is related to another object on any of the time frames that the object exists and zero (0) otherwise.

Type: Position, Over All Time

Last Relation Frame is the latest frame on which the object is related to another object across all time frames. The first frame of the dataset is considered frame 0.

Type: Count, Over All Time

Relation Primary Count is the total number of relations involving the object in which the object is in the primary set across all time frames.

Type: Count, Over All Time

Relation Secondary Count is the total number of relations involving the object in which the object is in the secondary/associate set across all time frames.

Type: Position, Per Time Point

Relative Acceleration is the acceleration of the secondary/associate object relative to its related, primary object and is calculated using the equation below, where Δt is the time between frames. Relative Acceleration is not calculated on the first two (2) frames in a set of consecutive frames over which objects are related, and the positions of parent objects are used if the there are any lineage splits for the objects of interest between the current frame and two (2) frames prior. Relative Acceleration is given for objects in the secondary/associate sets of relations.

Type: Position, Per Time Point

Relative Straight Line Velocity is the velocity of the secondary/associate object relative to its related, primary object based on the positions of both objects on the current frame and the earliest frame on which they are related. Relative Straight Line Velocity is not calculated on the first frame in a set of consecutive frames over which objects are related, and the positions of parent objects are used if the there are any lineage splits for the objects of interest between the current and previous frames. Relative Straight Line Velocity is given for secondary/associate objects.

Type: Position, Per Time Point

Relative Straight Line Velocity Squared is the square of the velocity of the secondary/associate object relative to its related, primary object based on the positions of both objects on the current frame and the earliest frame on which they are related. Relative Straight Line Velocity Squared is not calculated on the first frame in a set of consecutive frames over which objects are related, and the positions of parent objects are used if the there are any lineage splits for the objects of interest between the current and previous frames. Relative Straight Line Velocity Squared is given for secondary/associate objects.

Type: Position, Per Time Point

Relative Velocity is the velocity of the secondary/associate object relative to its related, primary object and is calculated using the equation below, where Δt is the time between frames. Relative Velocity is not calculated on the first frame in a set of consecutive frames over which objects are related, and the positions of parent objects are used if the there are any lineage splits for the objects of interest between the current and previous frames. Relative Velocity is given for objects in the secondary/associate sets of relations.

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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