The process of digitising histology slides involves multiple factors that can affect a whole slide image's (WSI) final appearance, including the staining protocol, scanner, and tissue type. This variability constitutes a domain shift and results in significant problems when training and testing deep learning (DL) algorithms in multi-cohort settings. As such, developing robust and generalisable DL models in computational pathology (CPath) remains an open challenge. In this regard, we propose a framework that generates stain-augmented versions of the training images using stain matrix perturbation. Thereafter, we employed a stain regularisation loss to enforce consistency between the feature representations of the source and augmented images. Doing so encourages the model to learn stain-invariant and, consequently, domain-invariant feature representations. We evaluate the performance of the proposed model on cross-domain multi-class tissue type classification of colorectal cancer images and have achieved improved performance compared to other state-of-the-art methods.

Deep learning models have shown immense promise in computational pathology (CPath) tasks, but their performance often suffers when applied to unseen data due to domain shifts. Addressing this requires domain generalization (DG) algorithms. However, a systematic evaluation of DG algorithms in the CPath context is lacking. This study aims to benchmark the effectiveness of 30 DG algorithms on 3 CPath tasks of varying difficulty through 7,560 cross-validation runs. We evaluate these algorithms using a unified and robust platform, incorporating modality-specific techniques and recent advances like pretrained foundation models. Our extensive cross-validation experiments provide insights into the relative performance of various DG strategies. We observe that self-supervised learning and stain augmentation consistently outperform other methods, highlighting the potential of pretrained models and data augmentation. Furthermore, we introduce a new pan-cancer tumor detection dataset (HISTOPANTUM) as a benchmark for future research. This study offers valuable guidance to researchers in selecting appropriate DG approaches for CPath tasks.

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 deep learning and handcrafted methods in terms of the quality of normalized images and in terms of downstream model performance on the CoNIC dataset.

Gastric and oesophageal (OG) cancers are the leading causes of cancer mortality worldwide. In OG cancers, recent studies have showed that PDL1 immune checkpoint inhibitors (ICI) in combination with chemotherapy improves patient survival. However, our understanding of the tumour immune microenvironment in OG cancers remains limited. In this study, we interrogate multiplex immunofluorescence (mIF) images taken from patients with advanced Oesophagogastric Adenocarcinoma (OGA) who received first-line fluoropyrimidine and platinum-based chemotherapy in the PLATFORM trial (NCT02678182) to predict the efficacy of the treatment and to explore the biological basis of patients responding to maintenance durvalumab (PDL1 inhibitor). Our proposed Artificial Intelligence (AI) based marker successfully identified responder from non-responder (p < 0.05) as well as those who could potentially benefit from ICI with statistical significance (p < 0.05) for both progression free and overall survival. Our findings suggest that T cells that express FOXP3 seem to heavily influence the patient treatment response and survival outcome. We also observed that higher levels of CD8+PD1+ cells are consistently linked to poor prognosis for both OS and PFS, regardless of ICI.

Digital pathology has gained significant traction in modern healthcare systems. This shift from optical microscopes to digital imagery brings with it the potential for improved diagnosis, efficiency, and the integration of AI tools into the pathologists workflow. A critical aspect of this is visualization. Throughout the development of a machine learning (ML) model in digital pathology, it is crucial to have flexible, openly available tools to visualize models, from their outputs and predictions to the underlying annotations and images used to train or test a model. We introduce TIAViz, a Python-based visualization tool built into TIAToolbox which allows flexible, interactive, fully zoomable overlay of a wide variety of information onto whole slide images, including graphs, heatmaps, segmentations, annotations and other WSIs. The UI is browser-based, allowing use either locally, on a remote machine, or on a server to provide publicly available demos. This tool is open source and is made available at: https://github.com/TissueImageAnalytics/tiatoolbox and via pip installation (pip install tiatoolbox) and conda as part of TIAToolbox.

Lung adenocarcinoma is a morphologically heterogeneous disease, characterized by five primary histologic growth patterns. The quantity of these patterns can be related to tumor behavior and has a significant impact on patient prognosis. In this work, we propose a novel machine learning pipeline capable of classifying tissue tiles into one of the five patterns or as non-tumor, with an Area Under the Receiver Operating Characteristic Curve (AUCROC) score of 0.97. Our model's strength lies in its comprehensive consideration of cellular spatial patterns, where it first generates cell maps from Hematoxylin and Eosin (H&E) whole slide images (WSIs), which are then fed into a convolutional neural network classification model. Exploiting these cell maps provides the model with robust generalizability to new data, achieving approximately 30% higher accuracy on unseen test-sets compared to current state of the art approaches. The insights derived from our model can be used to predict prognosis, enhancing patient outcomes.

Deep learning models have exhibited exceptional effectiveness in Computational Pathology (CPath) by tackling intricate tasks across an array of histology image analysis applications. Nevertheless, the presence of out-of-distribution data (stemming from a multitude of sources such as disparate imaging devices and diverse tissue preparation methods) can cause \emph{domain shift} (DS). DS decreases the generalization of trained models to unseen datasets with slightly different data distributions, prompting the need for innovative \emph{domain generalization} (DG) solutions. Recognizing the potential of DG methods to significantly influence diagnostic and prognostic models in cancer studies and clinical practice, we present this survey along with guidelines on achieving DG in CPath. We rigorously define various DS types, systematically review and categorize existing DG approaches and resources in CPath, and provide insights into their advantages, limitations, and applicability. We also conduct thorough benchmarking experiments with 28 cutting-edge DG algorithms to address a complex DG problem. Our findings suggest that careful experiment design and CPath-specific Stain Augmentation technique can be very effective. However, there is no one-size-fits-all solution for DG in CPath. Therefore, we establish clear guidelines for detecting and managing DS depending on different scenarios. While most of the concepts, guidelines, and recommendations are given for applications in CPath, we believe that they are applicable to most medical image analysis tasks as well.

Classification of gigapixel Whole Slide Images (WSIs) is an important prediction task in the emerging area of computational pathology. There has been a surge of research in deep learning models for WSI classification with clinical applications such as cancer detection or prediction of molecular mutations from WSIs. Most methods require expensive and labor-intensive manual annotations by expert pathologists. Weakly supervised Multiple Instance Learning (MIL) methods have recently demonstrated excellent performance; however, they still require large slide-level labeled training datasets that need a careful inspection of each slide by an expert pathologist. In this work, we propose a fully unsupervised WSI classification algorithm based on mutual transformer learning. Instances from gigapixel WSI (i.e., image patches) are transformed into a latent space and then inverse-transformed to the original space. Using the transformation loss, pseudo-labels are generated and cleaned using a transformer label-cleaner. The proposed transformer-based pseudo-label generation and cleaning modules mutually train each other iteratively in an unsupervised manner. A discriminative learning mechanism is introduced to improve normal versus cancerous instance labeling. In addition to unsupervised classification, we demonstrate the effectiveness of the proposed framework for weak supervision for cancer subtype classification as downstream analysis. Extensive experiments on four publicly available datasets show excellent performance compared to the state-of-the-art methods. We intend to make the source code of our algorithm publicly available soon.

International benchmarking competitions have become fundamental for the comparative performance assessment of image analysis methods. However, little attention has been given to investigating what can be learnt from these competitions. Do they really generate scientific progress? What are common and successful participation strategies? What makes a solution superior to a competing method? To address this gap in the literature, we performed a multi-center study with all 80 competitions that were conducted in the scope of IEEE ISBI 2021 and MICCAI 2021. Statistical analyses performed based on comprehensive descriptions of the submitted algorithms linked to their rank as well as the underlying participation strategies revealed common characteristics of winning solutions. These typically include the use of multi-task learning (63%) and/or multi-stage pipelines (61%), and a focus on augmentation (100%), image preprocessing (97%), data curation (79%), and postprocessing (66%). The "typical" lead of a winning team is a computer scientist with a doctoral degree, five years of experience in biomedical image analysis, and four years of experience in deep learning. Two core general development strategies stood out for highly-ranked teams: the reflection of the metrics in the method design and the focus on analyzing and handling failure cases. According to the organizers, 43% of the winning algorithms exceeded the state of the art but only 11% completely solved the respective domain problem. The insights of our study could help researchers (1) improve algorithm development strategies when approaching new problems, and (2) focus on open research questions revealed by this work.

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.