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.

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 and ISBI 2021 by releasing silver reference segmentation annotations for the training videos of 13 existing datasets, constructed using the submissions collected before October 1st, 2020, and by focusing on the development of methods that exhibit better generalizability and work across most, if not all, of the existing datasets, instead of being optimized for one or a few datasets only.

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.


New paper that analyzes the results collected over the 10-year existence of the challenge is out!


The website is currently under reconstruction and will be updated in July 2023! Nevertheless, the evaluation of on-line submissions keeps running on a monthly basis.