Lineages

Each of the .zip files in this dataset correspond to one of the microcolonies in the cib.zip file of the data repository of van Vliet et al (2017): https://zenodo.org/record/268921.

Files generally correspond to the standard FAST formats. However, to facilitate the benchmarking process, several copies of each type of file exist containing datasets processed in different ways. In general, these can be split into ground truth datasets (fully manually corrected), Corrected vs. automated analyses (differ in whether inputs to the modules were manually corrected or not) and all features vs. centroids only (differ in whether all features or just the centroids were used by the tracking module.

Specifically, each module is associated with the following files/directories:

Segmentations

Original_Segmentations: Segmentations as output directly by the FAST segmentation module.
Corrected_Segmentations: Segmentations corrected by hand.

Feature extraction

CellFeatures_AutoSeg.mat: Features extracted based on Original_Segmentations.
CellFeatures_ManualSeg.mat: Features extracted based on Corrected_Segmentations.

Tracking

Tracks_AutoSeg_Auto.mat: Automatically generated tracks output by the Tracking module with length, width, fluorescence and position as features and Original_Segmentations as the raw segmentations.
Tracks_AutoSeg_Auto_CentroidsOnly.mat: Automatically generated tracks output by the Tracking module with  only positional coordinates as features and Original_Segmentations as the raw segmentations.
Tracks_AutoSeg_Corrected.mat: Manually corrected ground truth for the tracks associated with Original_Segmentations. Generated with the track correction GUI.
Tracks_ManualSeg_Auto.mat: Automatically generated tracks output by the Tracking module with length, width, fluorescence and position as features and Corrected_Segmentations as the raw segmentations.
Tracks_ManualSeg_Corrected.mat: Manually corrected ground truth for the tracks associated with Corrected_Segmentations. Generated with the track correction GUI.

Divisions

Tracks_GoldStandardDivisions.mat: Manually corrected ground truth for division assignment, based on Tracks_ManualSeg_Corrected.mat.
Tracks_AutoStreamDivisions.mat: Automatically generated output of the division detection module using Tracks_AutoSeg_Auto.mat as input.
Tracks_AutoStreamDivisions_CentroidsOnly.mat: Automatically generated output of the division detection module using Tracks_AutoSeg_Auto_CentroidsOnly.mat as input.
Tracks_ManualStreamDivisions.mat: Automatically generated output of the division detection module using Tracks_ManualSeg_Corrected.mat as input.

In general, to use any one of these as an input to a later module, just rename the corresponding file to the FAST standard (e.g. rename Tracks_AutoSeg_Auto.mat to Tracks.mat to view the associated tracks in the overlays module). In some cases, you will also need to make sure that the Segmentation directory is filled with the corresponding segmentations (either Original or Corrected, depending on whether you are looking at the auto or the manual streams).