Data Structure

This section presents the dataframe columns of 2D and 3D data.

Note

Most of the columns are direct from SuperSegger and some are added during concatenation (bacteria.concatenate_clist()).

2D data

  • Cell ID - Unique cell identification

  • Cell birth time - The frame number in which the cell is born (min)

  • Cell age - The total time in which the cell “lived” or was identified

  • stat0 - Indicator of cell birth and division.

  • Long axis (L) birth - Length of the long axis of the cell at birth (px)

  • Long axis (L) death - Length of the long axis of the cell at division (px)

  • Short axis birth - Length of the short axis of the cell at birth (px)

  • Short axis death - Length of the short axis of the cell at division (px)

  • Area birth - Area of the cell at birth (px)

  • Area death - Area of the cell at division (px)

  • Fluor1 sum - Fluorescence intensity integrated over the cell area

  • Fluor1 mean - Average (by area) fluorescence intensity for the cell

  • Mother ID - “Cell ID” of this cell’s mother cell

  • Daughter1 ID - “Cell ID” of one daughter cell

  • Daughter2 ID - “Cell ID” of second daughter cell

  • L death / L birth - Ratio of long axis lengths in “Cell Division Time” and “Cell Birth Time”

  • Fluor1 sum death - Fluorescence intensity integrated over the cell area at cell division

  • Fluor1 mean death - Mean (by area) fluorescence intensity for the cell at division

  • Long axis/Short axis birth - Ratio of long to short axis lengths at birth

  • Long axis/Short axis death - Ratio of long to short axis lengths at division

  • Growth Rate - Average cell growth rate

  • Volume birth - Cell volume at birth (\(um^3\))

  • Volume division - Cell volume at division (\(um^3\))

  • Vd-Vb - Volume at division minus Volume at birth (\(um^3\))

  • fov - The field of view that this cell belongs to

  • Time Division - “Cell birth time” + “Cell age” (min)

Note

stat0 = 0 means no birth was observed, stat0 = 1 means no death/division was observed, stat0 = 2 means both birth and death were observed.

3D data

  • Cell ID - Unique cell identification

  • Long axis (L) - Length of the long axis at each time point (px)

  • Short axis - Length of the short axis at each time point (px)

  • Area - Area of the cell at each time point (px)

  • Fluor1 sum - Fluorescence intensity integrated over the cell area at each time point

  • Fluor1 mean - Average (by area) fluorescence intensity for the cell at each time point

  • Long axis length - Length of the long axis at each time point (px)

  • Time (Frames) - Frame reference for each feature (frames)

  • Age (Frames) - Cell age at each time point (frames)

  • Relative Age (Frames) - Cell age at each time point relative to the experiment (frames)

  • Time (fps) - Frame reference for each feature in minutes (min)

  • Age (fps) - Cell age at each time point in minutes (min)

  • Volume - Cell volume at each time point (\(um^3\))

  • fov - The field of view that this cell belongs to

  • F/V - Ratio between Fluorescence and Volume at each time point

  • Cell Cycle - The cell cycle in bins between 0 and 1