Accurate and efficient registration of whole slide images (WSIs) is essential for high-resolution, nuclei-level analysis in multi-stained tissue slides. We propose a novel coarse-to-fine framework CORE for accurate nuclei-level registration across diverse multimodal whole-slide image (WSI) datasets. The coarse registration stage leverages prompt-based tissue mask extraction to effectively filter out artefacts and non-tissue regions, followed by global alignment using tissue morphology and ac- celerated dense feature matching with a pre-trained feature extractor. From the coarsely aligned slides, nuclei centroids are detected and subjected to fine-grained rigid registration using a custom, shape-aware point-set registration model. Finally, non-rigid alignment at the cellular level is achieved by estimating a non-linear dis- placement field using Coherent Point Drift (CPD). Our approach benefits from automatically generated nuclei that enhance the accuracy of deformable registra- tion and ensure precise nuclei-level correspondence across modalities. The pro- posed model is evaluated on three publicly available WSI registration datasets, and two private datasets. We show that CORE outperforms current state-of-the-art methods in terms of generalisability, precision, and robustness in bright-field and immunofluorescence microscopy WSIs

Hematoxylin and eosin (H&E) staining visualizes histology but lacks specificity for diagnostic markers. Immunohistochemistry (IHC) staining provides protein-targeted staining but is restricted by tissue availability and antibody specificity. Virtual staining, i.e., computationally translating the H&E image to its IHC counterpart while preserving the tissue structure, is promising for efficient IHC generation. Existing virtual staining methods still face key challenges: 1) effective decomposition of staining style and tissue structure, 2) controllable staining process adaptable to diverse tissue and proteins, and 3) rigorous structural consistency modelling to handle the non-pixel-aligned nature of paired H&E and IHC images. This study proposes a mutual-information (MI)-guided score-based diffusion model for unpaired virtual staining. Specifically, we design 1) a global MI-guided energy function that disentangles the tissue structure and staining characteristics across modalities, 2) a novel timestep-customized reverse diffusion process for precise control of the staining intensity and structural reconstruction, and 3) a local MI-driven contrastive learning strategy to ensure the cellular level structural consistency between H&E-IHC images. Extensive experiments demonstrate the our superiority over state-of-the-art approaches, highlighting its biomedical potential. Codes will be open-sourced upon acceptance.

Whole slide image (WSI) classification is a critical task in computational pathology. However, the gigapixel-size of such images remains a major challenge for the current state of deep-learning. Current methods rely on multiple-instance learning (MIL) models with frozen feature extractors. Given the the high number of instances in each image, MIL methods have long assumed independence and permutation-invariance of patches, disregarding the tissue structure and correlation between patches. Recent works started studying this correlation between instances but the computational workload of such a high number of tokens remained a limiting factor. In particular, relative position of patches remains unaddressed. We propose to apply a straightforward encoding module, namely a RoFormer layer , relying on memory-efficient exact self-attention and relative positional encoding. This module can perform full self-attention with relative position encoding on patches of large and arbitrary shaped WSIs, solving the need for correlation between instances and spatial modeling of tissues. We demonstrate that our method outperforms state-of-the-art MIL models on three commonly used public datasets (TCGA-NSCLC, BRACS and Camelyon16)) on weakly supervised classification tasks. Code is available at https://github.com/Sanofi-Public/DDS-RoFormerMIL

The UNet architecture, based on Convolutional Neural Networks (CNN), has demonstrated its remarkable performance in medical image analysis. However, it faces challenges in capturing long-range dependencies due to the limited receptive fields and inherent bias of convolutional operations. Recently, numerous transformer-based techniques have been incorporated into the UNet architecture to overcome this limitation by effectively capturing global feature correlations. However, the integration of the Transformer modules may result in the loss of local contextual information during the global feature fusion process. To overcome these challenges, we propose a 2D medical image segmentation model called Multi-scale Cross Perceptron Attention Network (MCPA). The MCPA consists of three main components: an encoder, a decoder, and a Cross Perceptron. The Cross Perceptron first captures the local correlations using multiple Multi-scale Cross Perceptron modules, facilitating the fusion of features across scales. The resulting multi-scale feature vectors are then spatially unfolded, concatenated, and fed through a Global Perceptron module to model global dependencies. Furthermore, we introduce a Progressive Dual-branch Structure to address the semantic segmentation of the image involving finer tissue structures. This structure gradually shifts the segmentation focus of MCPA network training from large-scale structural features to more sophisticated pixel-level features. We evaluate our proposed MCPA model on several publicly available medical image datasets from different tasks and devices, including the open large-scale dataset of CT (Synapse), MRI (ACDC), fundus camera (DRIVE, CHASE_DB1, HRF), and OCTA (ROSE). The experimental results show that our MCPA model achieves state-of-the-art performance. The code is available at https://github.com/simonustc/MCPA-for-2D-Medical-Image-Segmentation.

We introduce a new benchmark dataset, Placenta, for node classification in an underexplored domain: predicting microanatomical tissue structures from cell graphs in placenta histology whole slide images. This problem is uniquely challenging for graph learning for a few reasons. Cell graphs are large (>1 million nodes per image), node features are varied (64-dimensions of 11 types of cells), class labels are imbalanced (9 classes ranging from 0.21% of the data to 40.0%), and cellular communities cluster into heterogeneously distributed tissues of widely varying sizes (from 11 nodes to 44,671 nodes for a single structure). Here, we release a dataset consisting of two cell graphs from two placenta histology images totalling 2,395,747 nodes, 799,745 of which have ground truth labels. We present inductive benchmark results for 7 scalable models and show how the unique qualities of cell graphs can help drive the development of novel graph neural network architectures.

Tissue awareness has a great demand to improve surgical accuracy in minimally invasive procedures. In arthroscopy, it is one of the challenging tasks due to surgical sites exhibit limited features and textures. Moreover, arthroscopic surgical video shows high intra-class variations. Arthroscopic videos are recorded with endoscope known as arthroscope which records tissue structures at proximity, therefore, frames contain minimal joint structure. As consequences, fully conventional network-based segmentation model suffers from long- and short- term dependency problems. In this study, we present a densely connected shape aware multi-scale segmentation model which captures multi-scale features and integrates shape features to achieve tissue-tool segmentations. The model has been evaluated with three distinct datasets. Moreover, with the publicly available polyp dataset our proposed model achieved 5.09 % accuracy improvement.

Knee arthroscopy is a minimally invasive surgical (MIS) procedure which is performed to treat knee-joint ailment. Lack of visual information of the surgical site obtained from miniaturized cameras make this surgical procedure more complex. Knee cavity is a very confined space; therefore, surgical scenes are captured at close proximity. Insignificant context of knee atlas often makes them unrecognizable as a consequence unintentional tissue damage often occurred and shows a long learning curve to train new surgeons. Automatic context awareness through labeling of the surgical site can be an alternative to mitigate these drawbacks. However, from the previous studies, it is confirmed that the surgical site exhibits several limitations, among others, lack of discriminative contextual information such as texture and features which drastically limits this vision task. Additionally, poor imaging conditions and lack of accurate ground-truth labels are also limiting the accuracy. To mitigate these limitations of knee arthroscopy, in this work we proposed a scene segmentation method that successfully segments multi structures.

Part of what fuels societal angst about the use of increasingly sophisticated, quasi-autonomous algorithms collectively known as AI is the fear that machines will supplant people in an ever-growing number of jobs. While this is undoubtedly true and has been for every prior generation of new technology from the power loom to the backhoe, the more significant question is whether AI replaces or merely displaces people? Namely, does it lead to the unemployed or to the differently employed. Medicine is one of the most promising areas of AI development and as I discussed last week, in hospitals and clinics there's a good argument that deep learning (DL) will augment human expertise, not supersede it. Ground zero of the DL disruption in medicine is imaging, however as my column pointed out, experts are optimistic that AI will make for better radiologists, not fewer.