NIS3D: A Completely Annotated Benchmark for Dense 3D Nuclei Image Segmentation

Despite the rapid advances of large-volume 3D imaging acquisition methods and the emergence of sophisticated algorithms to segment the nuclei in recent years, a benchmark with all cells completely annotated is still missing, making it hard to accurately assess and further improve the performance of the algorithms. The existing nuclei segmentation benchmarks either worked on 2D only or annotated a small number of 3D cells, perhaps due to the high cost of 3D annotation for large-scale data. To fulfill the critical need, we constructed NIS3D, a 3D, high cell density, large-volume, and completely annotated Nuclei Image Segmentation benchmark, assisted by our newly designed semi-automatic annotation software. NIS3D provides more than 22,000 cells across multiple most-used species in this area. Each cell is labeled by three independent annotators, so we can measure the variability of each annotation.