Jinhee Lee

Jeongun Ryu, Aaron Valero Puche, JaeWoong Shin et al.

Cell detection is a fundamental task in computational pathology that can be used for extracting high-level medical information from whole-slide images. For accurate cell detection, pathologists often zoom out to understand the tissue-level structures and zoom in to classify cells based on their morphology and the surrounding context. However, there is a lack of efforts to reflect such behaviors by pathologists in the cell detection models, mainly due to the lack of datasets containing both cell and tissue annotations with overlapping regions. To overcome this limitation, we propose and publicly release OCELOT, a dataset purposely dedicated to the study of cell-tissue relationships for cell detection in histopathology. OCELOT provides overlapping cell and tissue annotations on images acquired from multiple organs. Within this setting, we also propose multi-task learning approaches that benefit from learning both cell and tissue tasks simultaneously. When compared against a model trained only for the cell detection task, our proposed approaches improve cell detection performance on 3 datasets: proposed OCELOT, public TIGER, and internal CARP datasets. On the OCELOT test set in particular, we show up to 6.79 improvement in F1-score. We believe the contributions of this paper, including the release of the OCELOT dataset at https://lunit-io.github.io/research/publications/ocelot are a crucial starting point toward the important research direction of incorporating cell-tissue relationships in computation pathology.

JaeWoong Shin, Jeongun Ryu, Aaron Valero Puche et al.

Pathologists routinely alternate between different magnifications when examining Whole-Slide Images, allowing them to evaluate both broad tissue morphology and intricate cellular details to form comprehensive diagnoses. However, existing deep learning-based cell detection models struggle to replicate these behaviors and learn the interdependent semantics between structures at different magnifications. A key barrier in the field is the lack of datasets with multi-scale overlapping cell and tissue annotations. The OCELOT 2023 challenge was initiated to gather insights from the community to validate the hypothesis that understanding cell and tissue (cell-tissue) interactions is crucial for achieving human-level performance, and to accelerate the research in this field. The challenge dataset includes overlapping cell detection and tissue segmentation annotations from six organs, comprising 673 pairs sourced from 306 The Cancer Genome Atlas (TCGA) Whole-Slide Images with hematoxylin and eosin staining, divided into training, validation, and test subsets. Participants presented models that significantly enhanced the understanding of cell-tissue relationships. Top entries achieved up to a 7.99 increase in F1-score on the test set compared to the baseline cell-only model that did not incorporate cell-tissue relationships. This is a substantial improvement in performance over traditional cell-only detection methods, demonstrating the need for incorporating multi-scale semantics into the models. This paper provides a comparative analysis of the methods used by participants, highlighting innovative strategies implemented in the OCELOT 2023 challenge.

Min-Kook Choi, Jaehyeong Park, Jihun Jung et al.

One of the most important factors in training object recognition networks using convolutional neural networks (CNNs) is the provision of annotated data accompanying human judgment. Particularly, in object detection or semantic segmentation, the annotation process requires considerable human effort. In this paper, we propose a semi-supervised learning (SSL)-based training methodology for object detection, which makes use of automatic labeling of un-annotated data by applying a network previously trained from an annotated dataset. Because an inferred label by the trained network is dependent on the learned parameters, it is often meaningless for re-training the network. To transfer a valuable inferred label to the unlabeled data, we propose a re-alignment method based on co-occurrence matrix analysis that takes into account one-hot-vector encoding of the estimated label and the correlation between the objects in the image. We used an MS-COCO detection dataset to verify the performance of the proposed SSL method and deformable neural networks (D-ConvNets) as an object detector for basic training. The performance of the existing state-of-the-art detectors (DConvNets, YOLO v2, and single shot multi-box detector (SSD)) can be improved by the proposed SSL method without using the additional model parameter or modifying the network architecture.