Phase retrieval in inline holography is a fundamental yet ill-posed inverse problem due to the nonlinear coupling between amplitude and phase in coherent imaging. We present a novel off-the-shelf solution that leverages a diffusion model trained solely on object amplitude to recover both amplitude and phase from diffraction intensities. Using a predictor-corrector sampling framework with separate likelihood gradients for amplitude and phase, our method enables complex field reconstruction without requiring ground-truth phase data for training. We validate the proposed approach through extensive simulations and experiments, demonstrating robust generalization across diverse object shapes, imaging system configurations, and modalities, including lensless setups. Notably, a diffusion prior trained on simple amplitude data (e.g., polystyrene beads) successfully reconstructs complex biological tissue structures, highlighting the method's adaptability. This framework provides a cost-effective, generalizable solution for nonlinear inverse problems in computational imaging, and establishes a foundation for broader coherent imaging applications beyond holography.

Glioblastoma, a highly aggressive brain tumor with diverse molecular and pathological features, poses a diagnostic challenge due to its heterogeneity. Accurate diagnosis and assessment of this heterogeneity are essential for choosing the right treatment and improving patient outcomes. Traditional methods rely on identifying specific features in tissue samples, but deep learning offers a promising approach for improved glioblastoma diagnosis. In this paper, we present our approach to the BraTS-Path Challenge 2024. We leverage a pre-trained model and fine-tune it on the BraTS-Path training dataset. Our model demonstrates poor performance on the challenging BraTS-Path validation set, as rigorously assessed by the Synapse online platform. The model achieves an accuracy of 0.392229, a recall of 0.392229, and a F1-score of 0.392229, indicating a consistent ability to correctly identify instances under the target condition. Notably, our model exhibits perfect specificity of 0.898704, showing an exceptional capacity to correctly classify negative cases. Moreover, a Matthews Correlation Coefficient (MCC) of 0.255267 is calculated, to signify a limited positive correlation between predicted and actual values and highlight our model's overall predictive power. Our solution also achieves the second place during the testing phase.

Virtual staining of tissue offers a powerful tool for transforming label-free microscopy images of unstained tissue into equivalents of histochemically stained samples. This study presents a diffusion model-based super-resolution virtual staining approach utilizing a Brownian bridge process to enhance both the spatial resolution and fidelity of label-free virtual tissue staining, addressing the limitations of traditional deep learning-based methods. Our approach integrates novel sampling techniques into a diffusion model-based image inference process to significantly reduce the variance in the generated virtually stained images, resulting in more stable and accurate outputs. Blindly applied to lower-resolution auto-fluorescence images of label-free human lung tissue samples, the diffusion-based super-resolution virtual staining model consistently outperformed conventional approaches in resolution, structural similarity and perceptual accuracy, successfully achieving a super-resolution factor of 4-5x, increasing the output space-bandwidth product by 16-25-fold compared to the input label-free microscopy images. Diffusion-based super-resolved virtual tissue staining not only improves resolution and image quality but also enhances the reliability of virtual staining without traditional chemical staining, offering significant potential for clinical diagnostics.

In recent years, the advent of spatial transcriptomics (ST) technology has unlocked unprecedented opportunities for delving into the complexities of gene expression patterns within intricate biological systems. Despite its transformative potential, the prohibitive cost of ST technology remains a significant barrier to its widespread adoption in large-scale studies. An alternative, more cost-effective strategy involves employing artificial intelligence to predict gene expression levels using readily accessible whole-slide images (WSIs) stained with Hematoxylin and Eosin (H\&E). However, existing methods have yet to fully capitalize on multimodal information provided by H&E images and ST data with spatial location. In this paper, we propose \textbf{mclSTExp}, a multimodal contrastive learning with Transformer and Densenet-121 encoder for Spatial Transcriptomics Expression prediction. We conceptualize each spot as a "word", integrating its intrinsic features with spatial context through the self-attention mechanism of a Transformer encoder. This integration is further enriched by incorporating image features via contrastive learning, thereby enhancing the predictive capability of our model. Our extensive evaluation of \textbf{mclSTExp} on two breast cancer datasets and a skin squamous cell carcinoma dataset demonstrates its superior performance in predicting spatial gene expression. Moreover, mclSTExp has shown promise in interpreting cancer-specific overexpressed genes, elucidating immune-related genes, and identifying specialized spatial domains annotated by pathologists. Our source code is available at https://github.com/shizhiceng/mclSTExp.

With the advent of novel cancer treatment options such as immunotherapy, studying the tumour immune micro-environment is crucial to inform on prognosis and understand response to therapeutic agents. A key approach to characterising the tumour immune micro-environment may be through combining (1) digitised microscopic high-resolution optical images of hematoxylin and eosin (H&E) stained tissue sections obtained in routine histopathology examinations with (2) automated immune cell detection and classification methods. However, current individual immune cell classification models for digital pathology present relatively poor performance. This is mainly due to the limited size of currently available datasets of individual immune cells, a consequence of the time-consuming and difficult problem of manually annotating immune cells on digitised H&E whole slide images. In that context, we introduce Immunocto, a massive, multi-million automatically generated database of 6,848,454 human cells, including 2,282,818 immune cells distributed across 4 subtypes: CD4$^+$ T cell lymphocytes, CD8$^+$ T cell lymphocytes, B cell lymphocytes, and macrophages. For each cell, we provide a 64$\times$64 pixels H&E image at $\mathbf{40}\times$ magnification, along with a binary mask of the nucleus and a label. To create Immunocto, we combined open-source models and data to automatically generate the majority of contours and labels. The cells are obtained from a matched H&E and immunofluorescence colorectal dataset from the Orion platform, while contours are obtained using the Segment Anything Model. A classifier trained on H&E images from Immunocto produces an average F1 score of 0.74 to differentiate the 4 immune cell subtypes and other cells. Immunocto can be downloaded at: https://zenodo.org/uploads/11073373.

Systemic amyloidosis is a group of diseases characterized by the deposition of misfolded proteins in various organs and tissues, leading to progressive organ dysfunction and failure. Congo red stain is the gold standard chemical stain for the visualization of amyloid deposits in tissue sections, as it forms complexes with the misfolded proteins and shows a birefringence pattern under polarized light microscopy. However, Congo red staining is tedious and costly to perform, and prone to false diagnoses due to variations in the amount of amyloid, staining quality and expert interpretation through manual examination of tissue under a polarization microscope. Here, we report the first demonstration of virtual birefringence imaging and virtual Congo red staining of label-free human tissue to show that a single trained neural network can rapidly transform autofluorescence images of label-free tissue sections into brightfield and polarized light microscopy equivalent images, matching the histochemically stained versions of the same samples. We demonstrate the efficacy of our method with blind testing and pathologist evaluations on cardiac tissue where the virtually stained images agreed well with the histochemically stained ground truth images. Our virtually stained polarization and brightfield images 1 highlight amyloid birefringence patterns in a consistent, reproducible manner while mitigating diagnostic challenges due to variations in the quality of chemical staining and manual imaging processes as part of the clinical workflow.

Single cell analysis of human skeletal muscle (SM) tissue cross-sections is a fundamental tool for understanding many neuromuscular disorders. For this analysis to be reliable and reproducible, identification of individual fibres within microscopy images (segmentation) of SM tissue should be automatic and precise. Biomedical scientists in this field currently rely on custom tools and general machine learning (ML) models, both followed by labour intensive and subjective manual interventions to fine-tune segmentation. We believe that fully automated, precise, reproducible segmentation is possible by training ML models. However, in this important biomedical domain, there are currently no good quality, publicly available annotated imaging datasets available for ML model training. In this paper we release NCL-SM: a high quality bioimaging dataset of 46 human SM tissue cross-sections from both healthy control subjects and from patients with genetically diagnosed muscle pathology. These images include $>$ 50k manually segmented muscle fibres (myofibres). In addition we also curated high quality myofibre segmentations, annotating reasons for rejecting low quality myofibres and low quality regions in SM tissue images, making these annotations completely ready for downstream analysis. This, we believe, will pave the way for development of a fully automatic pipeline that identifies individual myofibres within images of tissue sections and, in particular, also classifies individual myofibres that are fit for further analysis.

Single cell analysis of skeletal muscle (SM) tissue is a fundamental tool for understanding many neuromuscular disorders. For this analysis to be reliable and reproducible, identification of individual fibres within microscopy images (segmentation) of SM tissue should be precise. There is currently no tool or pipeline that makes automatic and precise segmentation and curation of images of SM tissue cross-sections possible. Biomedical scientists in this field rely on custom tools and general machine learning (ML) models, both followed by labour intensive and subjective manual interventions to get the segmentation right. We believe that automated, precise, reproducible segmentation is possible by training ML models. However, there are currently no good quality, publicly available annotated imaging datasets available for ML model training. In this paper we release NCL-SM: a high quality bioimaging dataset of 46 human tissue sections from healthy control subjects and from patients with genetically diagnosed muscle pathology. These images include $>$ 50k manually segmented muscle fibres (myofibres). In addition we also curated high quality myofibres and annotated reasons for rejecting low quality myofibres and regions in SM tissue images, making this data completely ready for downstream analysis. This, we believe, will pave the way for development of a fully automatic pipeline that identifies individual myofibres within images of tissue sections and, in particular, also classifies individual myofibres that are fit for further analysis.

While therapies for altering the immune composition, including immunotherapies, have shown exciting results for treating hematological cancers, they are less effective for immunologically-cold, solid tumors. Spatial omics technologies capture the spatial organization of the TME with unprecedented molecular detail, revealing the relationship between immune cell localization and molecular signals. Here, we formulate T-cell infiltration prediction as a self-supervised machine learning problem and develop a counterfactual optimization strategy that leverages large scale spatial omics profiles of patient tumors to design tumor perturbations predicted to boost T-cell infiltration. A convolutional neural network predicts T-cell distribution based on signaling molecules in the TME provided by imaging mass cytometry. Gradient-based counterfactual generation, then, computes perturbations predicted to boost T-cell abundance. We apply our framework to melanoma, colorectal cancer (CRC) liver metastases, and breast tumor data, discovering combinatorial perturbations predicted to support T-cell infiltration across tens to hundreds of patients. This work presents a paradigm for counterfactual-based prediction and design of cancer therapeutics using spatial omics data.

Melanoma is one of the most aggressive forms of skin cancer, causing a large proportion of skin cancer deaths. However, melanoma diagnoses by pathologists shows low interrater reliability. As melanoma is a cancer of the melanocyte, there is a clear need to develop a melanocytic cell segmentation tool that is agnostic to pathologist variability and automates pixel-level annotation. Gigapixel-level pathologist labeling, however, is impractical. Herein, we propose a means to train deep neural networks for melanocytic cell segmentation from hematoxylin and eosin (H&E) stained sections and paired immunohistochemistry (IHC) of adjacent tissue sections, achieving a mean IOU of 0.64 despite imperfect ground-truth labels.