CoNIC Challenge: Pushing the Frontiers of Nuclear Detection, Segmentation, Classification and Counting

Nuclear detection, segmentation and morphometric profiling are essential in helping us further understand the relationship between histology and patient outcome. To drive innovation in this area, we setup a community-wide challenge using the largest available dataset of its kind to assess nuclear segmentation and cellular composition. Our challenge, named CoNIC, stimulated the development of reproducible algorithms for cellular recognition with real-time result inspection on public leaderboards. We conducted an extensive post-challenge analysis based on the top-performing models using 1,658 whole-slide images of colon tissue. With around 700 million detected nuclei per model, associated features were used for dysplasia grading and survival analysis, where we demonstrated that the challenge's improvement over the previous state-of-the-art led to significant boosts in downstream performance. Our findings also suggest that eosinophils and neutrophils play an important role in the tumour microevironment. We release challenge models and WSI-level results to foster the development of further methods for biomarker discovery.

Color Space-based HoVer-Net for Nuclei Instance Segmentation and Classification

Nuclei segmentation and classification is the first and most crucial step that is utilized for many different microscopy medical analysis applications. However, it suffers from many issues such as the segmentation of small objects, imbalance, and fine-grained differences between types of nuclei. In this paper, multiple different contributions were done tackling these problems present. Firstly, the recently released "ConvNeXt" was used as the encoder for HoVer-Net model since it leverages the key components of transformers that make them perform well. Secondly, to enhance the visual differences between nuclei, a multi-channel color space-based approach is used to aid the model in extracting distinguishing features. Thirdly, Unified Focal loss (UFL) was used to tackle the background-foreground imbalance. Finally, Sharpness-Aware Minimization (SAM) was used to ensure generalizability of the model. Overall, we were able to outperform the current state-of-the-art (SOTA), HoVer-Net, on the preliminary test set of the CoNiC Challenge 2022 by 12.489% mPQ+.