We introduce LYSTO, the Lymphocyte Assessment Hackathon, which was held in conjunction with the MICCAI 2019 Conference in Shenzen (China). The competition required participants to automatically assess the number of lymphocytes, in particular T-cells, in histopathological images of colon, breast, and prostate cancer stained with CD3 and CD8 immunohistochemistry. Differently from other challenges setup in medical image analysis, LYSTO participants were solely given a few hours to address this problem. In this paper, we describe the goal and the multi-phase organization of the hackathon; we describe the proposed methods and the on-site results. Additionally, we present post-competition results where we show how the presented methods perform on an independent set of lung cancer slides, which was not part of the initial competition, as well as a comparison on lymphocyte assessment between presented methods and a panel of pathologists. We show that some of the participants were capable to achieve pathologist-level performance at lymphocyte assessment. After the hackathon, LYSTO was left as a lightweight plug-and-play benchmark dataset on grand-challenge website, together with an automatic evaluation platform. LYSTO has supported a number of research in lymphocyte assessment in oncology. LYSTO will be a long-lasting educational challenge for deep learning and digital pathology, it is available at https://lysto.grand-challenge.org/.
From the simple measurement of tissue attributes in pathology workflow to designing an explainable diagnostic/prognostic AI tool, access to accurate semantic segmentation of tissue regions in histology images is a prerequisite. However, delineating different tissue regions manually is a laborious, time-consuming and costly task that requires expert knowledge. On the other hand, the state-of-the-art automatic deep learning models for semantic segmentation require lots of annotated training data and there are only a limited number of tissue region annotated images publicly available. To obviate this issue in computational pathology projects and collect large-scale region annotations efficiently, we propose an efficient interactive segmentation network that requires minimum input from the user to accurately annotate different tissue types in the histology image. The user is only required to draw a simple squiggle inside each region of interest so it will be used as the guiding signal for the model. To deal with the complex appearance and amorph geometry of different tissue regions we introduce several automatic and minimalistic guiding signal generation techniques that help the model to become robust against the variation in the user input. By experimenting on a dataset of breast cancer images, we show that not only does our proposed method speed up the interactive annotation process, it can also outperform the existing automatic and interactive region segmentation models.
While high-resolution pathology images lend themselves well to `data hungry' deep learning algorithms, obtaining exhaustive annotations on these images is a major challenge. In this paper, we propose a self-supervised CNN approach to leverage unlabeled data for learning generalizable and domain invariant representations in pathology images. The proposed approach, which we term as Self-Path, is a multi-task learning approach where the main task is tissue classification and pretext tasks are a variety of self-supervised tasks with labels inherent to the input data. We introduce novel domain specific self-supervision tasks that leverage contextual, multi-resolution and semantic features in pathology images for semi-supervised learning and domain adaptation. We investigate the effectiveness of Self-Path on 3 different pathology datasets. Our results show that Self-Path with the domain-specific pretext tasks achieves state-of-the-art performance for semi-supervised learning when small amounts of labeled data are available. Further, we show that Self-Path improves domain adaptation for classification of histology image patches when there is no labeled data available for the target domain. This approach can potentially be employed for other applications in computational pathology, where annotation budget is often limited or large amount of unlabeled image data is available.
Object Segmentation is an important step in the work-flow of computational pathology. Deep learning based models as the best forming models require huge amount of labeled data for precise and reliable prediction. However, collecting labeled data is expensive, because it necessarily involves expert knowledge. This is perhaps best illustrated by medical tasks where measurements call for expensive machinery and labels are the fruit of a time-consuming analysis that draws from multiple human experts. As nuclei, cells and glands are fundamental objects for downstream analysis in histology, in this paper we propose a simple CNN-based approach to speed up collecting segmentation annotation for these objects by utilizing minimum input from an annotator. We show for nuclei and cells as small objects, one click inside objects is enough to have precise annotation. For glands as large objects, providing a squiggle to show the extend of gland can guide the model to outline the exact boundaries. This supervisory signals are fed to network as an auxiliary channels along with RGB channels. With detailed experiments, we show that our approach is generalizable, robust against variations in the user input and that it can be used to obtain annotations for completely different domains. Practically, a model trained on the masks generated by NuClick could achieve first rank in LYON19 challenge. Furthermore, as the output of our framework, we release two data-sets: 1) a dataset of lymphocyte annotations within IHC images and 2) a dataset of WBCs annotated in blood sample images.
The emerging area of computational pathology (CPath) is ripe ground for the application of deep learning (DL) methods to healthcare due to the sheer volume of raw pixel data in whole-slide images (WSIs) of cancerous tissue slides. However, it is imperative for the DL algorithms relying on nuclei-level details to be able to cope with data from `the clinical wild', which tends to be quite challenging. We study, and extend recently released PanNuke dataset consisting of ~200,000 nuclei categorized into 5 clinically important classes for the challenging tasks of segmenting and classifying nuclei in WSIs. Previous pan-cancer datasets consisted of only up to 9 different tissues and up to 21,000 unlabeled nuclei and just over 24,000 labeled nuclei with segmentation masks. PanNuke consists of 19 different tissue types that have been semi-automatically annotated and quality controlled by clinical pathologists, leading to a dataset with statistics similar to the clinical wild and with minimal selection bias. We study the performance of segmentation and classification models when applied to the proposed dataset and demonstrate the application of models trained on PanNuke to whole-slide images. We provide comprehensive statistics about the dataset and outline recommendations and research directions to address the limitations of existing DL tools when applied to real-world CPath applications.