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Reported Feature Explanations

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Atiyeh Ahmadi edited this page Jan 29, 2025 · 2 revisions

TrajectoryX, TrajectoryY

The differences in the x-coordinate and y-coordinate between:

  • The target bacterium and source bacterium of a continuity link.
  • The daughter and mother bacterium of a division link.

Unit: micrometer

Note: For unexpected beginning bacteria or those in the first time step of the dataset, this value is set to NaN.

Endpoint1_X, Endpoint1_Y, Endpoint2_X, Endpoint2_Y

Coordinates representing the two endpoints of a bacterium.

Unit: micrometer

id

A unique numerical identifier assigned to each bacterium for tracking throughout its lifecycle.

parent_id

The ID of the mother bacterium.

Note: For bacteria existing in the first time step or with unexpected beginnings, this value is set to 0.

divideFlag

Indicates whether a bacterium has undergone cell division:

  • True: Division occurred. This value is set for all records associated with the bacterium's lifecycle.
  • False: Division did not occur.

Division_TimeStep

The time step at which the bacterium divides, corresponding to the first frame of its daughters' lifecycle.

  • 0: If no division occurs.

Note: This value is set for all records associated with the mothers's lifecycle.

Daughter_Mother_Length_Ratio

The ratio of the length of a daughter bacterium to its mother during a division.

  • This value is only set in the record corresponding to the first time step of the daughter bacterium's life history.

Total_Daughter_Mother_Length_Ratio

The ratio of the total length of all daughters to the length of the mother bacterium.

  • This value is only set in the record corresponding to the last time step of the mother bacterium's life history.

Max_Daughter_Mother_Length_Ratio

The ratio of the maximum length of the daughters to the length of the mother bacterium.

  • This value is only set in the record corresponding to the last time step of the mother bacterium's life history.

Daughter_Avg_TrajectoryX

The average TrajectoryX of the daughter bacteria in a division.

  • This value is only set in the record corresponding to the last time step of the mother bacterium's life history.

Daughter_Avg_TrajectoryY

The average TrajectoryY of the daughter bacteria in a division.

  • This value is only set in the record corresponding to the last time step of the mother bacterium's life history.

Unexpected_End

True if the bacterium's lifecycle ends before the dataset's last frame and it does not divide.

  • This value is only set in the record corresponding to the last time step of the bacterium's life history.

Unexpected_Beginning

True if the bacterium does not have a source from the previous time step and appears after the first time step.

  • This value is only set in the record corresponding to the first time step of the bacterium's life history.

LifeHistory

The total number of time steps a bacterium has been alive.

  • Assigned to all records related to the bacterium's lifecycle.

Bacterium_Movement

The smallest displacement among the center and endpoints between:

  • The source bacterium and the target bacterium of a continuity link.

Unit: micrometer

Note: This value is set to NaN for:

  • Daughter - Mother division link.
  • Unexpected beginning Bacteria.
  • Bacteria in the first time step of dataset.

Bacterium_Slope

The slope of the line formed by the bacterium's endpoints.

Note: For vertical lines, this value is set to NaN.

Orientation_Angle_Between_Slopes

The orientation angle between the Bacteria_Slope of:

  • The target bacterium and the source bacterium in a continuity link
  • The daughter bacterium and the mother bacterium in a division link

Unit: degrees

Note:

  • For bacteria in the first time step of the dataset or unexpected beginnings, this value is NaN.
  • For bacteria where the Bacteria_Slope is 0, the value is 90°.

Length_Change_Ratio

The ratio of the target bacterium's length to the source bacterium's length in a continuity link.

Note: The value is set to NaN for:

  • Daughter bacteria at the moment of division
  • Unexpected beginning bacteria
  • Bacteria in the first time step of dataset
  • Bacteria with a Life_History of 1

Direction_of_Motion

The angle of motion is defined by the line connecting the center of the target-source in a continuity link or the daughter-mother in a division link.

Unit: radians

Note: The value is set to NaN for unexpected beginning bacteria or bacteria in the first time step of dataset.

Avg_Length_Change_Ratio

The average Length_Change_Ratio of a bacterium over its life.

Note: For bacteria with a Life_History of 1, this value is set to NaN.

cellAge

The age of a bacterium since its birth, measured in time steps.

radius

Half the minor axis length of the bacterium.

time

Represents the time step multiplied by the interval time, indicating the corresponding real time.

dir

A unit vector representing the orientation of the bacterium:

  • [cos("AreaShape_Orientation"), sin("AreaShape_Orientation")].

startVol

The length of the bacterium at the first time step of its life.

Note: This value is set for all records associated with the bacterium's lifecycle.

targetVol

The length of the bacterium at the last time step of its life.

Note: This value is set for all records associated with the bacterium's lifecycle.

Prev_ Features*

Properties of the bacterium from the previous time step:

  • Prev_Bacterium_Slope
  • Prev_MajorAxisLength (major axis length)
  • Prev_Center_X, Prev_Center_Y (center coordinate)
  • Prev_Endpoint1_X, Prev_Endpoint1_Y, Prev_Endpoint2_X, Prev_Endpoint2_Y (endpoints)

Notes:

  • For daughter bacteria at the moment of division, these parameters correspond to the mother's properties.
  • For unexpected beginning bacteria or bacteria in the first time step of the dataset, these values are NaN.

Neighbor_Difference_Count

The number of different neighboring bacteria between:

  • The target and the source of a continuity link
  • The daughter and the mother bacterium of a division link

Note: This value is set to 0 for unexpected beginning bacteria or bacteria in the first time step of dataset.

Neighbor_Shared_Count

The number of shared neighboring bacteria between:

  • The target and the source of a continuity link
  • The daughter and the mother bacterium of a division link

Note: This value is set to 0 for unexpected beginning bacteria or bacteria in the first time step of dataset.

Elongation_Rate

The elongation rate of a bacterium throughout its life cycle.

Unit: micrometer per minute

Note: This value is set for all records associated with the bacterium's lifecycle.

Velocity

The Velocity of a bacterium throughout its life cycle.

Unit: micrometer per minute

Note: This value is set for all records associated with the bacterium's lifecycle.

strainRate

The relative change in the bacterium's major axis length between the previous time step t−1 and the current time step t, normalized by the length at t−1.

strainRate_rolling

The average strain rate of the bacterium over its life history up to the current time step.

cellType

Classified cell type based on fluorescence intensity:

  • Type 3: Fluorescence intensities in at least two channels exceed the threshold.
  • Specific values (e.g., 2, 3, etc.): Assigned if the fluorescence intensity in only one channel exceeds the threshold..
  • Type 0: None of the fluorescence intensities exceed the threshold.

Source_Neighbor_Avg_TrajectoryX

The average TrajectoryX of the source bacterium's neighbors in links to the next time step.

Unit: micrometer

Source_Neighbor_Avg_TrajectoryY

The average TrajectoryY of the source bacterium's neighbors in links to the next time step.

Unit: micrometer

Motion_Alignment_Angle

The normalized angle (divided by 180°) between The trajectory vector of a link (continuity link or division link) and the average trajectory vector of the source bacterium's neighbors.

Average_Length

The average length of a bacterium measured throughout its life history.

Note: This value is set for all records associated with the bacterium's lifecycle.

Unit: micrometer

Division_Family_Count

The total number of divisions occurring within the family tree of a bacterium.

Note: This value is set for all records associated with the family tree.

Instant_Elongation_Rate

The elongation rate of a bacterium compared to the previous time step in its life history.

Note: For the first time step of the bacterium's life history, this value is NaN.

Unit: micrometer per minute

Instant_Velocity

The velocity of a bacterium compared to the previous time step in its life history.

Note: For the first time step of the bacterium's life history, this value is NaN.

Unit: micrometer per minute

Average_Instant_Velocity

The average Instant_Velocity of a bacterium calculated over its entire life history.

Note: For bacteria with a life history of one, the value is NaN.

Unit: micrometer per minute

Converted Units:

The units of the following columns have been converted from pixels to micrometers using the conversion factor provided by the user as input to TrackRefiner:

  • AreaShape_Center_X, AreaShape_Center_Y, Location_Center_X, Location_Center_Y (center coordinates of bacteria)
  • AreaShape_MajorAxisLength
  • AreaShape_MinorAxisLength

Additionally, the AreaShape_Orientation column has been converted from degrees to radians using the following formula:

$$ \text{Orientation (radian)} = -\frac{(\text{Orientation (degrees)} + 90) \cdot \pi}{180} $$

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