Particle

NAME [name]

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id

The unique Id of the particle

.

name

The name of the particle

CLUMP

The finite number of portion of a specified area inside the particle.

SHAPE [morphology]

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angularity  [mean]

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mean

The mean value of the curvature (defined as the reciprocal of the radius of curvature) values measured along the medial axis of the Particle

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max

The max value of the curvature values used to generate the mean angularity

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min

The min value of the curvature values used to generate the mean angularity

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median

The median value of the curvature values used to generate the mean angularity

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mid

The angularity value measured at the center of the medial axis

.

stdev

The standard deviation of the curvature values used to generate the mean angularity

.

variation

The ratio of the standard deviation and the mean value of the angularity

.

area

The area of the Particle in square pixels or in calibrated square units

.

aspectRatio

The aspect ratio of the particle’s fitted ellipse (see ImageJ Documention for more details)

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circularity

4π × area / perimeter2 with a value of 1.0 indicating a perfect circle (see ImageJ Documention for more details)

.

curvature

The curvature (defined as the reciprocal of the radius of curvature) measured between the end points and the center of the medial axis

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feret [max]

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max

The longest distance between any two points along the particle boundary, also known as maximum caliper

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min

The minimum caliper diameter

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length

The length of the medial axis of the particle in pixels or in calibrated units

.

morphology

The morphology index the particle is associated to

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perimeter

The length in pixels or in calibrated square units of the outside boundary of the particle

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roundness

4 × area / (π × major axis2) or the inverse of aspectRatio (see ImageJ Documention for more details)

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sinuosity

The ratio of the curvilinear length (along the medial axis) and the distance (straight line) between the end points of the medial axis

.

solidity

area / convex area (see ImageJ Documention for more details)

.

width [mean]

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mean

The mean value of the width in pixels or in calibrated units along the medial axis of the particle

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max

The max value of the width values used to generate the mean width

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min

The min value of the width values used to generate the mean width

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median

The median value of the width values used to generate the mean width

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mid

The width value measured at the center of the medial axis

.

stdev

The standard deviation of the width values used to generate the mean width

.

variation

The ratio of the standard deviation and the mean value of the width

LOCATION  [(x;y)]

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x

The x coordinate of the particle center, expressed in pixels or in calibrated units.

.

y

The y coordinate of the particle center, expressed in pixels or in calibrated units.

EXPERIMENT

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name

The name of the experiment

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description

The description of the experiment

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fullName

The name and the description of the experiment

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date

The date when the experiment was analyzed

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id

The unique Id of the experiment

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field

The field of the image used to analyze the experiment

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serie

The serie of the image used to analyze the experiment

IMAGE [label]

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name

The name the image

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label

The label of the frame on which the particle was detected

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meta

The metadata of the frame on which the particle was detected

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background

.

chX [mean]

The statistics of the gray values within the particle boundary measured on the channel X in the stack or hyperstack

.

count

The number of pixels within the particle boundary

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dmode

Most frequently occurring gray value within the particle boundary. Corresponds to the highest peak in the histogram (see ImageJ Documention for more details)

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kurtosis

The fourth order moment about the mean

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max

Maximum gray value within the particle boundary

.

mean

Average gray value within the particle boundary. This is the sum of the gray values of all the pixels in the selection divided by the number of pixels (see ImageJ Documention for more details)

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median

median gray value within the particle boundary

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min

Minimum gray value within the particle boundary

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skewness

The third order moment about the mean  (see ImageJ Documention for more details)

.

stdev

Standard deviation of the gray values used to generate the mean gray value

POSITION [position]

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position

The position (slice or frame) of the particle in the hyperstack

.

slice

The slice position of the particle in the hyperstack

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frame

The frame position of the particle in the hyperstack

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channel

The channel position of the particle in the hyperstack

INTENSITY

The average gray value measured on the channel used to detect the particle

.

chX [mean]

The statistics of the gray values within the particle boundary measured on the channel X in the stack or hyperstack

.

count

The number of pixels within the particle boundary

.

dmode

Most frequently occurring gray value within the particle boundary. Corresponds to the highest peak in the histogram (see ImageJ Documention for more details)

.

kurtosis

The fourth order moment about the mean

.

max

Maximum gray value within the particle boundary

.

mean

Average gray value within the particle boundary. This is the sum of the gray values of all the pixels in the selection divided by the number of pixels (see ImageJ Documention for more details)

.

mean_c

The corrected average gray value (mean_c=|(µparticle-µbackground))

.

median

median gray value within the particle boundary

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min

Minimum gray value within the particle boundary

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skewness

The third order moment about the mean  (see ImageJ Documention for more details)

.

signal

Is true [1] when  the unsigned sigma distance (z=|(µparticle-µbackground)/σbackground|) is higher than the user-defined value of z

.

snr

The signal-to-noise ratio between the average  gray value within the particle boundary and the average  gray value of the background

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sum

The sum of the gray values within the particle boundary

.

stdev

Standard deviation of the gray values used to generate the mean gray value

MAXIMA [count]

The properties of the associations with all the maxima

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betwixt

The number of maxima localized neither at one of the poles nor at the midcell region of the particle (see the Association section for more details)

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bipolar

Is true [1] when the particle is associated with at least two maxima localized at two different poles

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connected

Is true [1] when the particle is associated with at least one maximum associated with at least one other particle

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count

The total number of associated maxima.

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midcell

The number of maxima localized at the midcell region (see the Association section for more details)

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polar

The number of maxima localized at one of the poles (see the Association section for more details)

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pole[X]

The number of maxima localized at the specified pole (see the Orientationsection to see how to define poles indexes)

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type

The type of the association : none / unipolar / bipolar

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undefined

The number of maxima  with an undefined localization

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unipolar

Is true [1] when the particle is associated with at least two maxima localized at the same pole

.

distance  [mean]

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mean

The mean value of the distance in pixels or in calibrated units between the associated maxima

.

max

The maximum value of the distance values

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min

The minimum value of the distance values

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median

The median value of the distance values

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stdev

The standard deviation value of the distance values

.

variation

The ratio of the standard deviation and the mean value

.

X  [count]

The properties of the associations with the maxima detected using the settings defined at the index X

.

SEPTUM [count]

The number of septa detected along the medial axis of the particle (see the Septum detection section for more details)

PARENT [name]

The properties of the association with the parent particle (i.e. Bacteria) (see the Association section for more details)

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id

The unique Id of the parent particle

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name

The name of the parent particle

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location

.

cartesian [x;y]

.

x

The relative X-coordinate of the particle using the cartesian coordinate system

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y

The relative Y-coordinate of the particle using the cartesian coordinate system

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orthogonal [x;y;z]

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x

The relative X-coordinate of the particle using the orthogonal coordinate system

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y

The relative Y-coordinate of the particle using the orthogonal coordinate system

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z

The relative Z-coordinate of the particle using the orthogonal coordinate system

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normalized [x;y;z]

.

x

The relative X-coordinate of the particle using the normalized orthogonal coordinate system

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y

The relative Y-coordinate of the particle using the normalized orthogonal coordinate system

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z

The relative Z-coordinate of the particle using the normalized orthogonal coordinate system

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cylindrical [θ;r;p]

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theta

The angular position θ of the particle using a polar coordinate system [-π/2,π/2]

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p

The longitudinal position p of the particle using a polar coordinate system [-1,1]

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r

The radial coordinate r of the particle using the cylindrical coordinate system [-1,1]

.

b

The revolution angle β of the particle using a polar coordinate system [0,2π]

.

l

The arc length L of the particle using a polar coordinate system.

.

phi

The elevation angle ϕ of the particle using a polar coordinate system [-π/2,π/2]

.

distance

.

center

The distance in pixels or in calibrated units between the orthogonal projection of the particle center and the center of the parent particle

.

pole1

The distance in pixels or in calibrated units between the orthogonal projection of the particle center and the tip of the pole 1

.

pole2

The distance in pixels or in calibrated units between the orthogonal projection of the particle center and the tip of the pole 2

.

side

The distance in pixels or in calibrated units between the particle center and the closest side of the parent particle

.

axis

The distance in pixels or in calibrated units between the particle center and its orthogonal projection on the medial axis of the parent particle

.

linker

The distance in pixels or in calibrated units between the particle center and the point of reference on the parent particle

.

localization [title]

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title

The localization of the particle inside the parent particle ('polar','midcell','betwixt','undefined')

.

index

The index of the localization of the particle inside the parent particle (polar:0,midcell:1,betwixt:2,undefined:3)

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side

Is true [1] when the particle is located close to the sides of the parent particle (location.norm.y>=0.5)

.

axis

Is true [1] when the particle is located close to the medial axis of the parent particle (location.norm.y<0.5)

.

inside

Is true [1] when the particle is located inside the parent particle

.

outside

Is true [1] when the particle is located outside the parent particle

.

branch

The index of the branch that the particle is associated with

.

pole

The index of the pole that the particle is associated with

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midcell

Is true [1] when the particle localization is 'midcell'

.

polar

Is true [1] when the particle localization is 'polar'

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betwixt

Is true [1] when the particle localization is 'betwixt'

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tip

Is true [1] when the particle is located at the tip of one of the poles of the parent particle

CONTACT [count]

.

active

The number of accepted cells in contact with the Particle

.

morphologyX

The number of cells matching the morphology X in contact with the Particle

.

total

The total number of cells (accepted and refused) in contact with the Particle

TYPE

.

color

The color of the associated type

.

index

The index of the associated type

.

title

The title of the associated type

DISTANCE [mean]

.

mean

The average distance between the particle and the surrounding particles

.

stdev

The standard deviation of the distances  between the particle and the surrounding particles

.

count

The number of surrounding particles

GAUSSIAN [fit]

.

a

The amplitude of the peak

.

b

The offset of the peak

.

d

The standard deviation of the peak

.

x

The x-position of the center of the peak

.

y

The y-position of the center of the peak

.

fit

Is true [1] when the amplitude is greater than the specified threshold