Aivia Software
Measurement definitions
This page has definitions for measurements found in the General tab of the Measurements window. The Measurements window is accessed through the Measurement Tool icon in the Spreadsheet. The Object Classifier and some recipes automatically generate Advanced Measurements, and the equations for such measurements are shown in the Advanced tab of the Measurements window. Custom measurements can also be added, removed, and edited in the Advanced tab. Colocalization measurements can be added in the Colocal tab.
Outline
Outlines are 2D objects defined by closed sets of line segments.
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.
On this page:
- 1 Outline
- 2 Mesh
- 3 Track
- 3.1 Lineage
- 4 Neuron
- 5 Whole cell
- 5.1 Cell membrane
- 5.2 Nuclear membrane
- 5.3 Vesicle
- 5.4 Cell
- 5.5 Cytoplasm
- 5.6 Nucleus
- 6 Relation
- 6.1 Track relation
- 7 References
- 8 Related articles
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. |