Tracking Data I/II of the publication "A graph-based cell tracking algorithm with few manually tunable parameters and automated segmentation error correction"

DATA belonging to the paper
"A graph-based cell tracking algorithm with few manually tunable parameters and automated segmentation error correction"
Katharina Löffler, Tim Scherr, Ralf Mikut
doi: https://doi.org/10.1101/2021.03.16.435631

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To investigate the influence of different segmentation errors on the tracking performance we simulate errorneous segmentation data:
- under-segmentation (referred to as "merge" in the folders), over-segmentation("split"), False Negatives ("remove"), combination of the aforementioned errors ("mixed")
- percentages: 1,2,5,10,20 of errorneous masks per dataset
- runs: 5 randomly initialized runs per combination
- datasets: Fluo-N2DH-SIM+ and Fluo-N3DH-SIM+ each with two image sequences
---> in total 4 (error types) * 5 (percentage) * 5 (runs) * 2 (data sets) * 2 (image sequences) = 400 datasets

The datasets can be recreated by running our code https://git.scc.kit.edu/KIT-Sch-GE/2021-cell-tracking
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RESULTS
We evuated the four tracking algorithms KIT-Sch-GE(1), KTH-SE, MU-Lux-CZ and our proposed algorithm on the aforementioned datasets and compare their performance using the CTC metrics DET, SEG and TRA.
This repository contains all metrics as xls files and all tracking results as image sequences.

xls files
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compare_all_trackers_on_synt_bm.csv
Comparing the tracking algorithms MU-Lux-CZ, KTH-SE, KIT-Sch-GE(1) and the proposed tracking algorithm on synthetically degraded segmentation data Fluo-N2DH-SIM+ and Fluo-N3DH-SIM+ (Cell Tracking Challenge datasets).
Reported scores are DET, SEG and TRA from the Cell Tracking Challenge
(Fig8 and Fig9 and Supplementary Figures 3 and 4 are created from this data)

compare_postprocessing_on_synth_bm.csv
Comparing the different post-processing strategies of the proposed tracking algorithm algorithm on synthetically degraded segmentation data Fluo-N2DH-SIM+ and Fluo-N3DH-SIM+ (Cell Tracking Challenge datasets).
Reported scores are DET, SEG and TRA from the Cell Tracking Challenge
(Fig7 and Fig8 and Supplementary Figures 1 and 2 are created from this data)

PLEASE NOTE: the folder compare_postprocessing_synth_bm  is provided in the repository 10.5281/zenodo.5227610 due to size restrictions.

folders (decompressed approximately 90GB of data!)
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tracking_data
    compare_all_synth_bm
    Contains all tracking results for each tracking algorithm on the synthetically degraded datasets ()

    compare_all_synth_bm_no_error
    Contains the tracking results for each tracking algorithm provided with the perfect ground truth segmentation data

    compare_postprocessing_synth_bm [will be stored in 10.5281/zenodo.5227610 due to size restrictions]
    Contains all tracking resuls for each postprocessing configuration of the proposed cell tracking algorithm
    the leaf folders are names run_xPOSTPROCESSING where x is the run number and POSTPROCESSING the postprocessing key
    Postprocessing keys: ("no untangle" or "no masks" is indicated by an overline in the paper)
    all ("untangle + masks" in the paper)
    nd ("no untangle + masks")
    nd_ns-l ("no untangle + no masks")
    ns-l ("untangle + no masks")