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Export

Export

For further use in data analysis, some metrics on colonies can be exported. This is based on colonies that were already found in the program. This page describes the export options. Most variables are exported as a three-column table, containing the frame number, the colony number and the exported data of interest, grouped with similar variables. See SI Fig. 4 from manuscript for some illustration on colonies.

Export menu

Export window overview

Metadata export

This option exports several analysis parameters that were used for analysis, including (when relevant):

  • total image number
  • image folder
  • the spatial calibration factor (pxl to µm conversion rate)
  • plate radius and position, or region of interest polygon vertices
  • image mode (grayscale or RGB)
  • detection radius threshold
  • time of data export

Export options

Data delimiter in the CSV and export unit (µm / pxl) can be set. A subpart of the data can be exported rather than the whole data, on specific frames (images) or colonies. For this, specify numbers in one of those formats:

  • a list of frames/colonies spearated by commas e.g. 1,3,4,6,8 => values outside range will be ignored
  • a list in the form Start:Gap:End, e.g. 2:3:13 will export 2,5,8,11.
  • for colonies, a list number identifier, specified as a single negative value (for list identifiers, see main GUI. The existing lists are showed in the Export window under "User Lists", see below)

Growth parameters

Those are the parameters obtained as explained in depth in original article, when calculated:

  • Appearance time is the time at which colony size reaches the defined threshold
  • Growth rate is the growth rate obtained from time-lapse images or overlaying pictures
  • Radius of a given colony at a given frame
  • (X,Y) positions of colonies in the picture

User lists

This option exports lists as binary values (0: not on list, 1: on list) corresponding to Userlists. This includes:

  • the lists manually set by user
  • the warning lists that were automatically generated by the program:
    • growth curve detection failure (failed Kymograph)
    • colonies in close range to each other ("near col")

Density metrics

Various metrics quantifying the density of colonies can be selected for export. Note that apart from the Voronoi area they are directly calculated when executing the data export according to the user wishes, and recalculated at each export, which may be lengthy for large images or high colony numbers.

Shape and color

Various shape and color metrics quantifying the color and shape of colonies can be selected for export. As the dentity metrics, they are calculated when executing the data export, and recalculated at each export.