StainFuser: Controlling Diffusion for Faster Neural Style Transfer in Multi-Gigapixel Histology Images

Stain normalization algorithms aim to transform the color and intensity characteristics of a source multi-gigapixel histology image to match those of a target image, mitigating inconsistencies in the appearance of stains used to highlight cellular components in the images. We propose a new approach, StainFuser, which treats this problem as a style transfer task using a novel Conditional Latent Diffusion architecture, eliminating the need for handcrafted color components. With this method, we curate SPI-2M the largest stain normalization dataset to date of over 2 million histology images with neural style transfer for high-quality transformations. Trained on this data, StainFuser outperforms current state-of-the-art GAN and handcrafted methods in terms of the quality of normalized images. Additionally, compared to existing approaches, it improves the performance of nuclei instance segmentation and classification models when used as a test time augmentation method on the challenging CoNIC dataset. Finally, we apply StainFuser on multi-gigapixel Whole Slide Images (WSIs) and demonstrate improved performance in terms of computational efficiency, image quality and consistency across tiles over current methods.

Scene Graph Aided Radiology Report Generation

Radiology report generation (RRG) methods often lack sufficient medical knowledge to produce clinically accurate reports. The scene graph contains rich information to describe the objects in an image. We explore enriching the medical knowledge for RRG via a scene graph, which has not been done in the current RRG literature. To this end, we propose the Scene Graph aided RRG (SGRRG) network, a framework that generates region-level visual features, predicts anatomical attributes, and leverages an automatically generated scene graph, thus achieving medical knowledge distillation in an end-to-end manner. SGRRG is composed of a dedicated scene graph encoder responsible for translating the scene graph, and a scene graph-aided decoder that takes advantage of both patch-level and region-level visual information. A fine-grained, sentence-level attention method is designed to better dis-till the scene graph information. Extensive experiments demonstrate that SGRRG outperforms previous state-of-the-art methods in report generation and can better capture abnormal findings.

Can Prompt Learning Benefit Radiology Report Generation?

Radiology report generation aims to automatically provide clinically meaningful descriptions of radiology images such as MRI and X-ray. Although great success has been achieved in natural scene image captioning tasks, radiology report generation remains challenging and requires prior medical knowledge. In this paper, we propose PromptRRG, a method that utilizes prompt learning to activate a pretrained model and incorporate prior knowledge. Since prompt learning for radiology report generation has not been explored before, we begin with investigating prompt designs and categorise them based on varying levels of knowledge: common, domain-specific and disease-enriched prompts. Additionally, we propose an automatic prompt learning mechanism to alleviate the burden of manual prompt engineering. This is the first work to systematically examine the effectiveness of prompt learning for radiology report generation. Experimental results on the largest radiology report generation benchmark, MIMIC-CXR, demonstrate that our proposed method achieves state-of-the-art performance. Code will be available upon the acceptance.

LYSTO: The Lymphocyte Assessment Hackathon and Benchmark Dataset

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/.

Nuclear Segmentation and Classification: On Color & Compression Generalization

Since the introduction of digital and computational pathology as a field, one of the major problems in the clinical application of algorithms has been the struggle to generalize well to examples outside the distribution of the training data. Existing work to address this in both pathology and natural images has focused almost exclusively on classification tasks. We explore and evaluate the robustness of the 7 best performing nuclear segmentation and classification models from the largest computational pathology challenge for this problem to date, the CoNIC challenge. We demonstrate that existing state-of-the-art (SoTA) models are robust towards compression artifacts but suffer substantial performance reduction when subjected to shifts in the color domain. We find that using stain normalization to address the domain shift problem can be detrimental to the model performance. On the other hand, neural style transfer is more consistent in improving test performance when presented with large color variations in the wild.

CAMANet: Class Activation Map Guided Attention Network for Radiology Report Generation

Radiology report generation (RRG) has gained increasing research attention because of its huge potential to mitigate medical resource shortages and aid the process of disease decision making by radiologists. Recent advancements in Radiology Report Generation (RRG) are largely driven by improving models' capabilities in encoding single-modal feature representations, while few studies explore explicitly the cross-modal alignment between image regions and words. Radiologists typically focus first on abnormal image regions before they compose the corresponding text descriptions, thus cross-modal alignment is of great importance to learn an abnormality-aware RRG model. Motivated by this, we propose a Class Activation Map guided Attention Network (CAMANet) which explicitly promotes cross-modal alignment by employing the aggregated class activation maps to supervise the cross-modal attention learning, and simultaneously enriches the discriminative information. Experimental results demonstrate that CAMANet outperforms previous SOTA methods on two commonly used RRG benchmarks.

Lane Change Classification and Prediction with Action Recognition Networks

Anticipating lane change intentions of surrounding vehicles is crucial for efficient and safe driving decision making in an autonomous driving system. Previous works often adopt physical variables such as driving speed, acceleration and so forth for lane change classification. However, physical variables do not contain semantic information. Although 3D CNNs have been developing rapidly, the number of methods utilising action recognition models and appearance feature for lane change recognition is low, and they all require additional information to pre-process data. In this work, we propose an end-to-end framework including two action recognition methods for lane change recognition, using video data collected by cameras. Our method achieves the best lane change classification results using only the RGB video data of the PREVENTION dataset. Class activation maps demonstrate that action recognition models can efficiently extract lane change motions. A method to better extract motion clues is also proposed in this paper.

Cross-modal Prototype Driven Network for Radiology Report Generation

Radiology report generation (RRG) aims to describe automatically a radiology image with human-like language and could potentially support the work of radiologists, reducing the burden of manual reporting. Previous approaches often adopt an encoder-decoder architecture and focus on single-modal feature learning, while few studies explore cross-modal feature interaction. Here we propose a Cross-modal PROtotype driven NETwork (XPRONET) to promote cross-modal pattern learning and exploit it to improve the task of radiology report generation. This is achieved by three well-designed, fully differentiable and complementary modules: a shared cross-modal prototype matrix to record the cross-modal prototypes; a cross-modal prototype network to learn the cross-modal prototypes and embed the cross-modal information into the visual and textual features; and an improved multi-label contrastive loss to enable and enhance multi-label prototype learning. XPRONET obtains substantial improvements on the IU-Xray and MIMIC-CXR benchmarks, where its performance exceeds recent state-of-the-art approaches by a large margin on IU-Xray and comparable performance on MIMIC-CXR.

A QuadTree Image Representation for Computational Pathology

The field of computational pathology presents many challenges for computer vision algorithms due to the sheer size of pathology images. Histopathology images are large and need to be split up into image tiles or patches so modern convolutional neural networks (CNNs) can process them. In this work, we present a method to generate an interpretable image representation of computational pathology images using quadtrees and a pipeline to use these representations for highly accurate downstream classification. To the best of our knowledge, this is the first attempt to use quadtrees for pathology image data. We show it is highly accurate, able to achieve as good results as the currently widely adopted tissue mask patch extraction methods all while using over 38% less data.

Semantic annotation for computational pathology: Multidisciplinary experience and best practice recommendations

Recent advances in whole slide imaging (WSI) technology have led to the development of a myriad of computer vision and artificial intelligence (AI) based diagnostic, prognostic, and predictive algorithms. Computational Pathology (CPath) offers an integrated solution to utilize information embedded in pathology WSIs beyond what we obtain through visual assessment. For automated analysis of WSIs and validation of machine learning (ML) models, annotations at the slide, tissue and cellular levels are required. The annotation of important visual constructs in pathology images is an important component of CPath projects. Improper annotations can result in algorithms which are hard to interpret and can potentially produce inaccurate and inconsistent results. Despite the crucial role of annotations in CPath projects, there are no well-defined guidelines or best practices on how annotations should be carried out. In this paper, we address this shortcoming by presenting the experience and best practices acquired during the execution of a large-scale annotation exercise involving a multidisciplinary team of pathologists, ML experts and researchers as part of the Pathology image data Lake for Analytics, Knowledge and Education (PathLAKE) consortium. We present a real-world case study along with examples of different types of annotations, diagnostic algorithm, annotation data dictionary and annotation constructs. The analyses reported in this work highlight best practice recommendations that can be used as annotation guidelines over the lifecycle of a CPath project.