Exported data - nimwegenLab/moma GitHub Wiki

About

This section describes data files that MoMA exports for downstream analysis.

Export data folder (export_data__*)

This is an example of exported files in folder export_data__*:

Screenshot of exported files

Upon export the output folder will contain the following files:

  • CellStats__*.csv: This contains measured values. Each column contains a different measurement-type. Each row corresponds to a cell-instance, where the cell-ID column indicates which rows belong to the same cell. Here is a brief description of what each column / measurement type contains:
    • lane_ID: string identifier of the growth-lane within the mother machine measurement. Example: pos_0_GL_7 : growth-lane 7 of position 0.
    • cell_ID: unique integer specifying a cell within the GL.
    • frame: integer indicating the frame in the time-lapse movie (1-based index).
    • cell_rank: position / rank of the cell withing the GL starting from the closed end of the GL. Example: A cell with rank 3 has 2 cells "below" it in direction of the closed end of the GL.
    • genealogy: string specifying the genealogy of a cell. Example: 4BBTBT would indicate that the cell: cell with rank 4 in first movie -> bottom daughter -> bottom daughter -> top daughter -> bottom daughter -> top daughter
    • type_of_end: indicates how the cell-track (i.e. all instances with same cell_ID) terminates. div: division assignment; map: mapping assignment; exit: exit assignment; lysis: lysis assignment; eod: end of measurement / movie
    • parent_ID: cell_ID of the parent cell
    • cells_in_lane: total number of cells in the lane

Track data folder (track_data__*)

  • <probability map filename>: This TIFF stack contains the probability map for each frame of the input images, as output by the U-Net segmentation model. Pixels this image have a value range from 0 to 1, where 0 is background and 1 is foreground (i.e. cell).
  • <cell masks filename>: This TIFF stack contains the labelled cell masks. Label values correspond to values cell-id column in the CSV file. The TIFF stack contains two slices per time-step. The first slice contains the cell-id of a connected component in the current frame and the second slice indicates contains the cell-id of the same component in the previous time-step. This allows mapping dividing cells to their parent in the previous frame.