Segmenting and tracking moving cells in time-lapse video sequences is a challenging task, required for many applications in both scientific and industrial settings. Properly characterizing how cells change shapes and move as they interact with their surrounding environment is key to understanding the mechanobiology of cell migration and its multiple implications in both normal tissue development and many diseases. In this challenge, we objectively compare and evaluate state-of-the-art whole-cell and nucleus segmentation and tracking methods using both real (2D and 3D) time-lapse microscopy videos of cells and nuclei, along with computer-generated (2D and 3D) video sequences simulating whole cells and nuclei moving in realistic environments.

The first edition of Cell Tracking Challenge was held under the auspices of the IEEE International Symposium on Biomedical Imaging (ISBI) in San Francisco in April 2013. The second and third editions were hosted by ISBI 2014 in Beijing and ISBI 2015 in New York. The report on the three challenge editions was published in Nature Methods. Since February 21st, 2017 the challenge is open for online submissions that are monthly evaluated and ranked.

One Challenge, Two Benchmarks: In October 2018 a new “spin-off” time-lapse cell segmentation benchmark was launched to address numerous requests for benchmarking only cell segmentation methods. This activity was initially hosted by ISBI 2019 in Venice in April 2019, and extended within ISBI 2020 by releasing silver reference segmentation annotations for the training videos of nine existing datasets, constructed using the submissions collected before September 1st, 2019. Both the Cell Tracking Benchmark (CTB) and the Cell Segmentation Benchmark (CSB) continue running online and share the same datasets. To take part in one or both of these benchmarks, you can freely download the Datasets but you need to register to submit your results for evaluation.

6th Challenge Edition at ISBI 2021: The sixth challenge edition is being organized as part of ISBI 2021 to be held virtually in April 2021. In this edition, the primary focus is put on methods that exhibit better generalizability and work across most, if not all, of the 13 already existing datasets, instead of developing methods optimized for one or a few datasets only. To this end, new silver reference segmentation annotations will be released for the training videos of all real datasets with complete gold reference tracking annotations available, being constructed using the submissions benchmarked before October 1st, 2020. The submissions will be evaluated and announced at the corresponding ISBI 2021 challenge workshop according to the ISBI 2021 challenge schedule, with a paper that reports on the results collected since the third edition being co-authored by ten best performers within the primary track of this sixth challenge edition and published in a top-tier journal afterward. Click here for more details!

Please note that participants, not interested in the sixth challenge edition, can submit their results for evaluation any time. However, in the case of exploiting the new silver reference segmentation annotations or submitting results for the newly added Fluo-C2DL-Huh7 dataset, the scores achieved will be provided after ISBI 2021.

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