Data for - Tracking one-in-a-million: Large-scale benchmark for microbial single-cell tracking with experiment-aware robustness metrics
DOI10.5281/zenodo.7260137Zenodo7260137MaRDI QIDQ6703046FDOQ6703046
Dataset published at Zenodo repository.
Katharina Löffler, Tim Scherr, Johannes Seiffarth, Luisa Blöbaum, Ralf Mikut, Alexander Grünberger, Katharina Nöh, Hanno Scharr
Publication date: 28 October 2022
Copyright license: Creative Commons Attribution 4.0 International
Large-scale Corynebacterium glutamicum data set with Segmentation and Tracking Annotation We provide five time-lapse sequences with manually corrected segmentation and tracking annotations of growingC. glutamicumcultivations. The dataset contains more than 1.4 million cell observations in 29k cell tracks and 14k cell divisions. We provide videos of the annotations (videos.zip) and the dataset inCell Tracking Challengeformat (ctc_format.zip). In the videos, cell contours are rendered in yellow, cell links between frames are colored red and cell divisions, and their links are colored in blue. Data Acquisition Corynebacterium glutamicumATCC 13032 was cultivated in BHI-medium at 30C in this study. From and overnight preculture, the main culture was inoculated the next day with a starting OD600 of 0.05 and grown at 120 rpm to a OD600 of 0.25. A chip was fabricated, according to(Tuber et al., 2020), and fixed to the microscopes holder. The main culture cells were transferred to monolayer growth chambers (height = 720 nm) on the microfluidic chip. Flow through the microfluidic device was mediated by pressure driven pumps with a pressure of 100 mbar on the medium reservoir. The time-lapse phase contrast images of five monolayer growth chambers were taken every minute using an inverted microscope (Nikon Eclipse Ti2) with a 100x oil emersion objective and a DS-QI2 camera (Nikon) at 15 % relative DIA-illumination intensity and 100 ms exposure time. The spatial image resolution is 0.072 m/px.
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