Daily Papers

Computational pathology relies on effective representation learning to support cancer research and precision medicine. Although self-supervised learning has driven major progress at the patch and whole-slide image levels, representation learning at the single-cell level remains comparatively underexplored, despite its importance for characterizing cell types and cellular phenotypes. We introduce LEMON (Learning Embeddings from Morphology Of Nuclei), a self-supervised foundation model for scalable single-cell image representation learning. Trained on millions of cell images from diverse tissues and cancer types, LEMON learns robust and versatile morphological representations that support large-scale single-cell analyses in pathology. We evaluate LEMON on five benchmark datasets across a range of prediction tasks and show that it provides strong performance, highlighting its potential as a new paradigm for cell-level computational pathology. Model weights are available at https://huggingface.co/aliceblondel/LEMON.

Cervical cytology presents a fundamentally ambiguous diagnostic landscape, where equivocal categories such as Atypical Squamous Cells of Undetermined Significance (ASC-US) occupy a morphological grey zone that is definitional. For clinical decision support, the goal extends beyond assigning a definitive label to every sample: cases must also be distinguished by whether the available evidence supports a confident decision or warrants further consideration, a distinction conventional classification models are not designed to explicitly represent. We propose a multiscale evidential framework that models cervical cytology along an ordinal disease continuum using clinically grounded soft anchors, representing progression from benign reactive changes to precancerous lesions and malignancy. Three biologically motivated spatial contexts--nuclear morphology, cytoplasmic characteristics, and neighbourhood cellular architecture--are independently encoded using a shared frozen DINOv2 backbone, preserving inter-scale disagreement that early fusion may obscure. Calibrated predictions are transformed into Dempster--Shafer belief masses and fused with reliability discounting, allowing conflicting evidence and insufficient support to remain explicitly uncommitted rather than forcing a decision. The fused belief state drives interpretable routing that separates confidently classified cases from those with irreducible evidential insufficiency, enabling clinically meaningful triage. Across two independent publicly available conventional cytology datasets, RIVA and CRIC Cervix, the framework generalises consistently, with uncertainty strongly associated with diagnostic difficulty: incorrect predictions carry 1.94x-4.13x higher uncertainty than correct ones.

Computational pathology models infer biologically and clinically meaningful outcomes from histology, but their predictions are shaped by complex, intertwined tissue signals whose roles are important to understand. Common pixel- and feature-space perturbations can produce implausible tissue, making model responses difficult to interpret. We introduce CPathOGen, a conditional latent-diffusion framework for generating paired H\&E counterfactuals with explicit controls over cellular spatial organization, nuclear morphology, and stain appearance. Cellular maps condition spatial structure through a spatial encoder, while a morphology/appearance vector modulates denoising through blockwise feature-wise linear modulation (FiLM). On held-out H\&E tiles, CPathOGen generates visually plausible tissue with improved distributional agreement after spatially guided selection, as reflected by lower Fréchet Inception Distance (FID) and Kernel Inception Distance (KID); generated cells track requested abundance and position, and measured morphology and color vary monotonically with their controls. We use these verified interventions to probe pathology encoders with endpoint heads, task-specific classifiers, and survival models. Responses are quantified using total variation distance and prediction-flip rate. We further introduce the Biology-Nuisance Sensitivity Ratio, a metric that contrasts model sensitivity to biologically motivated morphology and spatial factors with sensitivity to non-biological, stain-related nuisance variation. CPathOGen provides a practical, fidelity-audited framework for evaluating robustness and controlled feature sensitivity in computational pathology model. https://github.com/a12dongithub/PathOGen{GitHub} and https://huggingface.co/a12donhf/CPathOGen{Hugging~Face}.

Separating and labeling each instance of a nucleus (instance-aware segmentation) is the key challenge in segmenting single cell nuclei on fluorescence microscopy images. Deep Neural Networks can learn the implicit transformation of a nuclear image into a probability map indicating the class membership of each pixel (nucleus or background), but the use of post-processing steps to turn the probability map into a labeled object mask is error-prone. This especially accounts for nuclear images of tissue sections and nuclear images across varying tissue preparations. In this work, we aim to evaluate the performance of state-of-the-art deep learning architectures to segment nuclei in fluorescence images of various tissue origins and sample preparation types without post-processing. We compare architectures that operate on pixel to pixel translation and an architecture that operates on object detection and subsequent locally applied segmentation. In addition, we propose a novel strategy to create artificial images to extend the training set. We evaluate the influence of ground truth annotation quality, image scale and segmentation complexity on segmentation performance. Results show that three out of four deep learning architectures (U-Net, U-Net with ResNet34 backbone, Mask R-CNN) can segment fluorescent nuclear images on most of the sample preparation types and tissue origins with satisfactory segmentation performance. Mask R-CNN, an architecture designed to address instance aware segmentation tasks, outperforms other architectures. Equal nuclear mean size, consistent nuclear annotations and the use of artificially generated images result in overall acceptable precision and recall across different tissues and sample preparation types.

Nuclear segmentation, classification and quantification within Haematoxylin & Eosin stained histology images enables the extraction of interpretable cell-based features that can be used in downstream explainable models in computational pathology (CPath). However, automatic recognition of different nuclei is faced with a major challenge in that there are several different types of nuclei, some of them exhibiting large intraclass variability. In this work, we propose an approach that combine Separable-HoverNet and Instance-YOLOv5 to indentify colon nuclei small and unbalanced. Our approach can achieve mPQ+ 0.389 on the Segmentation and Classification-Preliminary Test Dataset and r2 0.599 on the Cellular Composition-Preliminary Test Dataset on ISBI 2022 CoNIC Challenge.

Nuclear segmentation, classification and quantification within Haematoxylin & Eosin stained histology images enables the extraction of interpretable cell-based features that can be used in downstream explainable models in computational pathology (CPath). However, automatic recognition of different nuclei is faced with a major challenge in that there are several different types of nuclei, some of them exhibiting large intra-class variability. To help drive forward research and innovation for automatic nuclei recognition in CPath, we organise the Colon Nuclei Identification and Counting (CoNIC) Challenge. The challenge encourages researchers to develop algorithms that perform segmentation, classification and counting of nuclei within the current largest known publicly available nuclei-level dataset in CPath, containing around half a million labelled nuclei. Therefore, the CoNIC challenge utilises over 10 times the number of nuclei as the previous largest challenge dataset for nuclei recognition. It is important for algorithms to be robust to input variation if we wish to deploy them in a clinical setting. Therefore, as part of this challenge we will also test the sensitivity of each submitted algorithm to certain input variations.

Precise and scalable instance segmentation of cell nuclei is essential for computational pathology, yet gigapixel Whole-Slide Images pose major computational challenges. Existing approaches rely on patch-based processing and costly post-processing for instance separation, sacrificing context and efficiency. We introduce LSP-DETR (Local Star Polygon DEtection TRansformer), a fully end-to-end framework that uses a lightweight transformer with linear complexity to process substantially larger images without additional computational cost. Nuclei are represented as star-convex polygons, and a novel radial distance loss function allows the segmentation of overlapping nuclei to emerge naturally, without requiring explicit overlap annotations or handcrafted post-processing. Evaluations on PanNuke and MoNuSeg show strong generalization across tissues and state-of-the-art efficiency, with LSP-DETR being over five times faster than the next-fastest leading method. Code and models are available at https://github.com/RationAI/lsp-detr.

Histopathological analysis is a cornerstone of cancer diagnosis, with Hematoxylin and Eosin (H&E) staining routinely acquired for every patient to visualize cell morphology and tissue architecture. On the other hand, multiplex immunofluorescence (mIF) enables more precise cell type identification via proteomic markers, but has yet to achieve widespread clinical adoption due to cost and logistical constraints. To bridge this gap, we introduce MIPHEI (Multiplex Immunofluorescence Prediction from H&E), a U-Net-inspired architecture that integrates state-of-the-art ViT foundation models as encoders to predict mIF signals from H&E images. MIPHEI targets a comprehensive panel of markers spanning nuclear content, immune lineages (T cells, B cells, myeloid), epithelium, stroma, vasculature, and proliferation. We train our model using the publicly available ORION dataset of restained H&E and mIF images from colorectal cancer tissue, and validate it on two independent datasets. MIPHEI achieves accurate cell-type classification from H&E alone, with F1 scores of 0.88 for Pan-CK, 0.57 for CD3e, 0.56 for SMA, 0.36 for CD68, and 0.30 for CD20, substantially outperforming both a state-of-the-art baseline and a random classifier for most markers. Our results indicate that our model effectively captures the complex relationships between nuclear morphologies in their tissue context, as visible in H&E images and molecular markers defining specific cell types. MIPHEI offers a promising step toward enabling cell-type-aware analysis of large-scale H&E datasets, in view of uncovering relationships between spatial cellular organization and patient outcomes.

In computational pathology, automatic nuclei instance segmentation plays an essential role in whole slide image analysis. While many computerized approaches have been proposed for this task, supervised deep learning (DL) methods have shown superior segmentation performances compared to classical machine learning and image processing techniques. However, these models need fully annotated datasets for training which is challenging to acquire, especially in the medical domain. In this work, we release one of the biggest fully manually annotated datasets of nuclei in Hematoxylin and Eosin (H&E)-stained histological images, called NuInsSeg. This dataset contains 665 image patches with more than 30,000 manually segmented nuclei from 31 human and mouse organs. Moreover, for the first time, we provide additional ambiguous area masks for the entire dataset. These vague areas represent the parts of the images where precise and deterministic manual annotations are impossible, even for human experts. The dataset and detailed step-by-step instructions to generate related segmentation masks are publicly available at https://www.kaggle.com/datasets/ipateam/nuinsseg and https://github.com/masih4/NuInsSeg, respectively.

Accurate detection and segmentation of cell nuclei in volumetric (3D) fluorescence microscopy datasets is an important step in many biomedical research projects. Although many automated methods for these tasks exist, they often struggle for images with low signal-to-noise ratios and/or dense packing of nuclei. It was recently shown for 2D microscopy images that these issues can be alleviated by training a neural network to directly predict a suitable shape representation (star-convex polygon) for cell nuclei. In this paper, we adopt and extend this approach to 3D volumes by using star-convex polyhedra to represent cell nuclei and similar shapes. To that end, we overcome the challenges of 1) finding parameter-efficient star-convex polyhedra representations that can faithfully describe cell nuclei shapes, 2) adapting to anisotropic voxel sizes often found in fluorescence microscopy datasets, and 3) efficiently computing intersections between pairs of star-convex polyhedra (required for non-maximum suppression). Although our approach is quite general, since star-convex polyhedra include common shapes like bounding boxes and spheres as special cases, our focus is on accurate detection and segmentation of cell nuclei. Finally, we demonstrate on two challenging datasets that our approach (StarDist-3D) leads to superior results when compared to classical and deep learning based methods.

Nucleus segmentation is a challenging task due to the crowded distribution and blurry boundaries of nuclei. Recent approaches represent nuclei by means of polygons to differentiate between touching and overlapping nuclei and have accordingly achieved promising performance. Each polygon is represented by a set of centroid-to-boundary distances, which are in turn predicted by features of the centroid pixel for a single nucleus. However, using the centroid pixel alone does not provide sufficient contextual information for robust prediction and thus degrades the segmentation accuracy. To handle this problem, we propose a Context-aware Polygon Proposal Network (CPP-Net) for nucleus segmentation. First, we sample a point set rather than one single pixel within each cell for distance prediction. This strategy substantially enhances contextual information and thereby improves the robustness of the prediction. Second, we propose a Confidence-based Weighting Module, which adaptively fuses the predictions from the sampled point set. Third, we introduce a novel Shape-Aware Perceptual (SAP) loss that constrains the shape of the predicted polygons. Here, the SAP loss is based on an additional network that is pre-trained by means of mapping the centroid probability map and the pixel-to-boundary distance maps to a different nucleus representation. Extensive experiments justify the effectiveness of each component in the proposed CPP-Net. Finally, CPP-Net is found to achieve state-of-the-art performance on three publicly available databases, namely DSB2018, BBBC06, and PanNuke. Code of this paper is available at \url{https://github.com/csccsccsccsc/cpp-net

Nuclei detection and segmentation in hematoxylin and eosin-stained (H&E) tissue images are important clinical tasks and crucial for a wide range of applications. However, it is a challenging task due to nuclei variances in staining and size, overlapping boundaries, and nuclei clustering. While convolutional neural networks have been extensively used for this task, we explore the potential of Transformer-based networks in this domain. Therefore, we introduce a new method for automated instance segmentation of cell nuclei in digitized tissue samples using a deep learning architecture based on Vision Transformer called CellViT. CellViT is trained and evaluated on the PanNuke dataset, which is one of the most challenging nuclei instance segmentation datasets, consisting of nearly 200,000 annotated Nuclei into 5 clinically important classes in 19 tissue types. We demonstrate the superiority of large-scale in-domain and out-of-domain pre-trained Vision Transformers by leveraging the recently published Segment Anything Model and a ViT-encoder pre-trained on 104 million histological image patches - achieving state-of-the-art nuclei detection and instance segmentation performance on the PanNuke dataset with a mean panoptic quality of 0.50 and an F1-detection score of 0.83. The code is publicly available at https://github.com/TIO-IKIM/CellViT

The development of deep segmentation models for computational pathology (CPath) can help foster the investigation of interpretable morphological biomarkers. Yet, there is a major bottleneck in the success of such approaches because supervised deep learning models require an abundance of accurately labelled data. This issue is exacerbated in the field of CPath because the generation of detailed annotations usually demands the input of a pathologist to be able to distinguish between different tissue constructs and nuclei. Manually labelling nuclei may not be a feasible approach for collecting large-scale annotated datasets, especially when a single image region can contain thousands of different cells. However, solely relying on automatic generation of annotations will limit the accuracy and reliability of ground truth. Therefore, to help overcome the above challenges, we propose a multi-stage annotation pipeline to enable the collection of large-scale datasets for histology image analysis, with pathologist-in-the-loop refinement steps. Using this pipeline, we generate the largest known nuclear instance segmentation and classification dataset, containing nearly half a million labelled nuclei in H&E stained colon tissue. We have released the dataset and encourage the research community to utilise it to drive forward the development of downstream cell-based models in CPath.

Star-convex shapes arise across bio-microscopy and radiology in the form of nuclei, nodules, metastases, and other units. Existing instance segmentation networks for such structures train on densely labeled instances for each dataset, which requires substantial and often impractical manual annotation effort. Further, significant reengineering or finetuning is needed when presented with new datasets and imaging modalities due to changes in contrast, shape, orientation, resolution, and density. We present AnyStar, a domain-randomized generative model that simulates synthetic training data of blob-like objects with randomized appearance, environments, and imaging physics to train general-purpose star-convex instance segmentation networks. As a result, networks trained using our generative model do not require annotated images from unseen datasets. A single network trained on our synthesized data accurately 3D segments C. elegans and P. dumerilii nuclei in fluorescence microscopy, mouse cortical nuclei in micro-CT, zebrafish brain nuclei in EM, and placental cotyledons in human fetal MRI, all without any retraining, finetuning, transfer learning, or domain adaptation. Code is available at https://github.com/neel-dey/AnyStar.

Nucleus instance segmentation in histology images is crucial for a broad spectrum of clinical applications. Current dominant algorithms rely on regression of nuclear proxy maps. Distinguishing nucleus instances from the estimated maps requires carefully curated post-processing, which is error-prone and parameter-sensitive. Recently, the Segment Anything Model (SAM) has earned huge attention in medical image segmentation, owing to its impressive generalization ability and promptable property. Nevertheless, its potential on nucleus instance segmentation remains largely underexplored. In this paper, we present a novel prompt-driven framework that consists of a nucleus prompter and SAM for automatic nucleus instance segmentation. Specifically, the prompter learns to generate a unique point prompt for each nucleus while the SAM is fine-tuned to output the corresponding mask for the prompted nucleus. Furthermore, we propose the inclusion of adjacent nuclei as negative prompts to enhance the model's capability to identify overlapping nuclei. Without complicated post-processing, our proposed method sets a new state-of-the-art performance on three challenging benchmarks. Code is available at github.com/windygoo/PromptNucSeg

This study developed a novel method for detecting hypernuclear events recorded in nuclear emulsion sheets using machine learning techniques. The artificial neural network-based object detection model was trained on surrogate images created through Monte Carlo simulations and image-style transformations using generative adversarial networks. The performance of the proposed model was evaluated using alpha-decay events obtained from the J-PARC E07 emulsion data. The model achieved approximately twice the detection efficiency of conventional image processing and reduced the time spent on manual visual inspection by approximately 1/17. The established method was successfully applied to the detection of hypernuclear events. This approach is a state-of-the-art tool for discovering rare events recorded in nuclear emulsion sheets without any real data for training.

Instance segmentation and classification of nuclei is an important task in computational pathology. We show that StarDist, a deep learning nuclei segmentation method originally developed for fluorescence microscopy, can be extended and successfully applied to histopathology images. This is substantiated by conducting experiments on the Lizard dataset, and through entering the Colon Nuclei Identification and Counting (CoNIC) challenge 2022, where our approach achieved the first spot on the leaderboard for the segmentation and classification task for both the preliminary and final test phase.

Morphological traits are physical characteristics of biological organisms that provide vital clues on how organisms interact with their environment. Yet extracting these traits remains a slow, expert-driven process, limiting their use in large-scale ecological studies. A major bottleneck is the absence of high-quality datasets linking biological images to trait-level annotations. In this work, we demonstrate that sparse autoencoders trained on foundation-model features yield monosemantic, spatially grounded neurons that consistently activate on meaningful morphological parts. Leveraging this property, we introduce a trait annotation pipeline that localizes salient regions and uses vision-language prompting to generate interpretable trait descriptions. Using this approach, we construct Bioscan-Traits, a dataset of 80K trait annotations spanning 19K insect images from BIOSCAN-5M. Human evaluation confirms the biological plausibility of the generated morphological descriptions. We assess design sensitivity through a comprehensive ablation study, systematically varying key design choices and measuring their impact on the quality of the resulting trait descriptions. By annotating traits with a modular pipeline rather than prohibitively expensive manual efforts, we offer a scalable way to inject biologically meaningful supervision into foundation models, enable large-scale morphological analyses, and bridge the gap between ecological relevance and machine-learning practicality.

In this work we introduce a physically motivated method of performing disc/spheroid decomposition of simulated galaxies, which we apply to the Eagle sample. We make use of the HEALPix package to create Mollweide projections of the angular momentum map of each galaxy's stellar particles. A number of features arise on the angular momentum space which allows us to decompose galaxies and classify them into different morphological types. We assign stellar particles with angular separation of less/greater than 30 degrees from the densest grid cell on the angular momentum sphere to the disc/spheroid components, respectively. We analyse the spatial distribution for a subsample of galaxies and show that the surface density profiles of the disc and spheroid closely follow an exponential and a Sersic profile, respectively. In addition discs rotate faster, have smaller velocity dispersions, are younger and are more metal rich than spheroids. Thus our morphological classification reproduces the observed properties of such systems. Finally, we demonstrate that our method is able to identify a significant population of galaxies with counter-rotating discs and provide a more realistic classification of such systems compared to previous methods.

Automatic detection and segmentation of cells and nuclei in microscopy images is important for many biological applications. Recent successful learning-based approaches include per-pixel cell segmentation with subsequent pixel grouping, or localization of bounding boxes with subsequent shape refinement. In situations of crowded cells, these can be prone to segmentation errors, such as falsely merging bordering cells or suppressing valid cell instances due to the poor approximation with bounding boxes. To overcome these issues, we propose to localize cell nuclei via star-convex polygons, which are a much better shape representation as compared to bounding boxes and thus do not need shape refinement. To that end, we train a convolutional neural network that predicts for every pixel a polygon for the cell instance at that position. We demonstrate the merits of our approach on two synthetic datasets and one challenging dataset of diverse fluorescence microscopy images.

We present the data release for Galaxy Zoo 2 (GZ2), a citizen science project with more than 16 million morphological classifications of 304,122 galaxies drawn from the Sloan Digital Sky Survey. Morphology is a powerful probe for quantifying a galaxy's dynamical history; however, automatic classifications of morphology (either by computer analysis of images or by using other physical parameters as proxies) still have drawbacks when compared to visual inspection. The large number of images available in current surveys makes visual inspection of each galaxy impractical for individual astronomers. GZ2 uses classifications from volunteer citizen scientists to measure morphologies for all galaxies in the DR7 Legacy survey with m_r>17, in addition to deeper images from SDSS Stripe 82. While the original Galaxy Zoo project identified galaxies as early-types, late-types, or mergers, GZ2 measures finer morphological features. These include bars, bulges, and the shapes of edge-on disks, as well as quantifying the relative strengths of galactic bulges and spiral arms. This paper presents the full public data release for the project, including measures of accuracy and bias. The majority (>90%) of GZ2 classifications agree with those made by professional astronomers, especially for morphological T-types, strong bars, and arm curvature. Both the raw and reduced data products can be obtained in electronic format at http://data.galaxyzoo.org .

Nuclei segmentation and classification is a significant process in pathology image analysis. Deep learning-based approaches have greatly contributed to the higher accuracy of this task. However, those approaches suffer from the imbalanced nuclei data composition, which shows lower classification performance on the rare nuclei class. In this paper, we propose a realistic data synthesis method using a diffusion model. We generate two types of virtual patches to enlarge the training data distribution, which is for balancing the nuclei class variance and for enlarging the chance to look at various nuclei. After that, we use a semantic-label-conditioned diffusion model to generate realistic and high-quality image samples. We demonstrate the efficacy of our method by experiment results on two imbalanced nuclei datasets, improving the state-of-the-art networks. The experimental results suggest that the proposed method improves the classification performance of the rare type nuclei classification, while showing superior segmentation and classification performance in imbalanced pathology nuclei datasets.

Identifying and representing object instances such as cells or nuclei is a common task in microscopy image analysis. Established machine learning workflows typically use supervised detection or segmentation followed by feature extraction or classification, which requires manual annotations and treats instance segmentation and cell representation as separate stages. We describe a new unsupervised method for cell instance segmentation and phenotypic classification from unlabeled microscopy images. Our method is based on reconstructing each image using a coarse-to-fine routing pyramid that associates pixels with spatially sparse latent sources. The resulting pixel-to-latent associations yield instance masks, while the source latents encode cell morphology. We demonstrate competitive performance in instance segmentation across diverse cell morphologies and imaging modalities, as well as generative modeling of cellular phenotypes under perturbations. Source code and checkpoints are available at https://github.com/weigertlab/routing-pyramids.

Object segmentation is an important step in the workflow of computational pathology. Deep learning based models generally require large amount of labeled data for precise and reliable prediction. However, collecting labeled data is expensive because it often requires expert knowledge, particularly in medical imaging domain where labels are the result of a time-consuming analysis made by one or more human experts. As nuclei, cells and glands are fundamental objects for downstream analysis in computational pathology/cytology, in this paper we propose a simple CNN-based approach to speed up collecting annotations for these objects which requires minimum interaction from the annotator. We show that for nuclei and cells in histology and cytology images, one click inside each object is enough for NuClick to yield a precise annotation. For multicellular structures such as glands, we propose a novel approach to provide the NuClick with a squiggle as a guiding signal, enabling it to segment the glandular boundaries. These supervisory signals are fed to the network as auxiliary inputs along with RGB channels. With detailed experiments, we show that NuClick is adaptable to the object scale, robust against variations in the user input, adaptable to new domains, and delivers reliable annotations. An instance segmentation model trained on masks generated by NuClick achieved the first rank in LYON19 challenge. As exemplar outputs of our framework, we are releasing two datasets: 1) a dataset of lymphocyte annotations within IHC images, and 2) a dataset of segmented WBCs in blood smear images.

Nucleus detection and classification (NDC) in histopathology analysis is a fundamental task that underpins a wide range of high-level pathology applications. However, existing methods heavily rely on labor-intensive nucleus-level annotations and struggle to fully exploit large-scale unlabeled data for learning discriminative nucleus representations. In this work, we propose MUSE (MUlti-scale denSE self-distillation), a novel self-supervised learning method tailored for NDC. At its core is NuLo (Nucleus-based Local self-distillation), a coordinate-guided mechanism that enables flexible local self-distillation based on predicted nucleus positions. By removing the need for strict spatial alignment between augmented views, NuLo allows critical cross-scale alignment, thus unlocking the capacity of models for fine-grained nucleus-level representation. To support MUSE, we design a simple yet effective encoder-decoder architecture and a large field-of-view semi-supervised fine-tuning strategy that together maximize the value of unlabeled pathology images. Extensive experiments on three widely used benchmarks demonstrate that MUSE effectively addresses the core challenges of histopathological NDC. The resulting models not only surpass state-of-the-art supervised baselines but also outperform generic pathology foundation models.

Quantifying cell morphology using images and machine learning has proven to be a powerful tool to study the response of cells to treatments. However, models used to quantify cellular morphology are typically trained with a single microscopy imaging type. This results in specialized models that cannot be reused across biological studies because the technical specifications do not match (e.g., different number of channels), or because the target experimental conditions are out of distribution. Here, we present CHAMMI-75, an open access dataset of heterogeneous, multi-channel microscopy images from 75 diverse biological studies. We curated this resource from publicly available sources to investigate cellular morphology models that are channel-adaptive and can process any microscopy image type. Our experiments show that training with CHAMMI-75 can improve performance in multi-channel bioimaging tasks primarily because of its high diversity in microscopy modalities. This work paves the way to create the next generation of cellular morphology models for biological studies.

Masked image modelling (MIM) is a powerful self-supervised representation learning paradigm, whose potential has not been widely demonstrated in medical image analysis. In this work, we show the capacity of MIM to capture rich semantic representations of Haemotoxylin & Eosin (H&E)-stained images at the nuclear level. Inspired by Bidirectional Encoder representation from Image Transformers (BEiT), we split the images into smaller patches and generate corresponding discrete visual tokens. In addition to the regular grid-based patches, typically used in visual Transformers, we introduce patches of individual cell nuclei. We propose positional encoding of the irregular distribution of these structures within an image. We pre-train the model in a self-supervised manner on H&E-stained whole-slide images of diffuse large B-cell lymphoma, where cell nuclei have been segmented. The pre-training objective is to recover the original discrete visual tokens of the masked image on the one hand, and to reconstruct the visual tokens of the masked object instances on the other. Coupling these two pre-training tasks allows us to build powerful, context-aware representations of nuclei. Our model generalizes well and can be fine-tuned on downstream classification tasks, achieving improved cell classification accuracy on PanNuke dataset by more than 5% compared to current instance segmentation methods.

Cell instance segmentation in fluorescence microscopy images is becoming essential for cancer dynamics and prognosis. Data extracted from cancer dynamics allows to understand and accurately model different metabolic processes such as proliferation. This enables customized and more precise cancer treatments. However, accurate cell instance segmentation, necessary for further cell tracking and behavior analysis, is still challenging in scenarios with high cell concentration and overlapping edges. Within this framework, we propose a novel cell instance segmentation approach based on the well-known U-Net architecture. To enforce the learning of morphological information per pixel, a deep distance transformer (DDT) acts as a back-bone model. The DDT output is subsequently used to train a top-model. The following top-models are considered: a three-class (e.g., foreground, background and cell border) U-net, and a watershed transform. The obtained results suggest a performance boost over traditional U-Net architectures. This opens an interesting research line around the idea of injecting morphological information into a fully convolutional model.

Measuring the morphological parameters of galaxies is a key requirement for studying their formation and evolution. Surveys such as the Sloan Digital Sky Survey (SDSS) have resulted in the availability of very large collections of images, which have permitted population-wide analyses of galaxy morphology. Morphological analysis has traditionally been carried out mostly via visual inspection by trained experts, which is time-consuming and does not scale to large (gtrsim10^4) numbers of images. Although attempts have been made to build automated classification systems, these have not been able to achieve the desired level of accuracy. The Galaxy Zoo project successfully applied a crowdsourcing strategy, inviting online users to classify images by answering a series of questions. Unfortunately, even this approach does not scale well enough to keep up with the increasing availability of galaxy images. We present a deep neural network model for galaxy morphology classification which exploits translational and rotational symmetry. It was developed in the context of the Galaxy Challenge, an international competition to build the best model for morphology classification based on annotated images from the Galaxy Zoo project. For images with high agreement among the Galaxy Zoo participants, our model is able to reproduce their consensus with near-perfect accuracy (> 99%) for most questions. Confident model predictions are highly accurate, which makes the model suitable for filtering large collections of images and forwarding challenging images to experts for manual annotation. This approach greatly reduces the experts' workload without affecting accuracy. The application of these algorithms to larger sets of training data will be critical for analysing results from future surveys such as the LSST.

The galaxy population is strongly bimodal in both colour and morphology, and the two measures correlate strongly, with most blue galaxies being late-types (spirals) and most early-types, typically ellipticals, being red. This observation has led to the use of colour as a convenient selection criteria to make samples which are then labelled by morphology. Such use of colour as a proxy for morphology results in necessarily impure and incomplete samples. In this paper, we make use of the morphological labels produced by Galaxy Zoo to measure how incomplete and impure such samples are, considering optical (ugriz), NUV and NIR (JHK) bands. The best single colour optical selection is found using a threshold of g-r = 0.742, but this still results in a sample where only 56% of red galaxies are smooth and 56% of smooth galaxies are red. Use of the NUV gives some improvement over purely optical bands, particularly for late-types, but still results in low purity/completeness for early-types. No significant improvement is found by adding NIR bands. With any two bands, including NUV, a sample of early-types with greater than two-thirds purity cannot be constructed. Advances in quantitative galaxy morphologies have made colour-morphology proxy selections largely unnecessary going forward; where such assumptions are still required, we recommend studies carefully consider the implications of sample incompleteness/impurity.

Cell instance segmentation in cytology images has significant importance for biology analysis and cancer screening, while remains challenging due to 1) the extensive overlapping translucent cell clusters that cause the ambiguous boundaries, and 2) the confusion of mimics and debris as nuclei. In this work, we proposed a De-overlapping Network (DoNet) in a decompose-and-recombined strategy. A Dual-path Region Segmentation Module (DRM) explicitly decomposes the cell clusters into intersection and complement regions, followed by a Semantic Consistency-guided Recombination Module (CRM) for integration. To further introduce the containment relationship of the nucleus in the cytoplasm, we design a Mask-guided Region Proposal Strategy (MRP) that integrates the cell attention maps for inner-cell instance prediction. We validate the proposed approach on ISBI2014 and CPS datasets. Experiments show that our proposed DoNet significantly outperforms other state-of-the-art (SOTA) cell instance segmentation methods. The code is available at https://github.com/DeepDoNet/DoNet.

Pre-trained on a large and diverse dataset, the segment anything model (SAM) is the first promptable foundation model in computer vision aiming at object segmentation tasks. In this work, we evaluate SAM for the task of nuclear instance segmentation performance with zero-shot learning and finetuning. We compare SAM with other representative methods in nuclear instance segmentation, especially in the context of model generalisability. To achieve automatic nuclear instance segmentation, we propose using a nuclei detection model to provide bounding boxes or central points of nu-clei as visual prompts for SAM in generating nuclear instance masks from histology images.

Accurate detection and classification of nuclei in histopathology images are critical for diagnostic and research applications. We present KongNet, a multi-headed deep learning architecture featuring a shared encoder and parallel, cell-type-specialised decoders. Through multi-task learning, each decoder jointly predicts nuclei centroids, segmentation masks, and contours, aided by Spatial and Channel Squeeze-and-Excitation (SCSE) attention modules and a composite loss function. We validate KongNet in three Grand Challenges. The proposed model achieved first place on track 1 and second place on track 2 during the MONKEY Challenge. Its lightweight variant (KongNet-Det) secured first place in the 2025 MIDOG Challenge. KongNet pre-trained on the MONKEY dataset and fine-tuned on the PUMA dataset ranked among the top three in the PUMA Challenge without further optimisation. Furthermore, KongNet established state-of-the-art performance on the publicly available PanNuke and CoNIC datasets. Our results demonstrate that the specialised multi-decoder design is highly effective for nuclei detection and classification across diverse tissue and stain types. The pre-trained model weights along with the inference code have been publicly released to support future research.

The recent surge in performance for image analysis of digitised pathology slides can largely be attributed to the advances in deep learning. Deep models can be used to initially localise various structures in the tissue and hence facilitate the extraction of interpretable features for biomarker discovery. However, these models are typically trained for a single task and therefore scale poorly as we wish to adapt the model for an increasing number of different tasks. Also, supervised deep learning models are very data hungry and therefore rely on large amounts of training data to perform well. In this paper, we present a multi-task learning approach for segmentation and classification of nuclei, glands, lumina and different tissue regions that leverages data from multiple independent data sources. While ensuring that our tasks are aligned by the same tissue type and resolution, we enable meaningful simultaneous prediction with a single network. As a result of feature sharing, we also show that the learned representation can be used to improve the performance of additional tasks via transfer learning, including nuclear classification and signet ring cell detection. As part of this work, we train our developed Cerberus model on a huge amount of data, consisting of over 600K objects for segmentation and 440K patches for classification. We use our approach to process 599 colorectal whole-slide images from TCGA, where we localise 377 million, 900K and 2.1 million nuclei, glands and lumina, respectively and make the results available to the community for downstream analysis.

Histology images contain rich morphological information and can provide insights into pathological processes. However, deriving hypotheses relating morphological phenotypes to clinical attributes is bottlenecked by a manual image interpretation step. Here, we demonstrate that this process can be automated through interpretable deep learning. We present SCOPE, a method to interpret slide-level classifiers by combining pathology-specific vision--language models with sparse concept attribution onto a generalist histomorphological concept bank. To measure whether such explanations recover known morphology, we introduce MorphoRecoveryBench, a benchmark of seven tasks with pathologist-curated reference descriptions. On this benchmark, dense concept attribution is indistinguishable from a random baseline, whereas sparse attribution recovers substantial known morphology; decomposing the pooled slide embedding reaches similar explanation correctness at a fraction of the computational cost. Post-hoc interpretation of whole-slide classifiers can thus generate morphological hypotheses at scale, for expert validation.

Computer-aided histopathological image analysis for cancer detection is a major research challenge in the medical domain. Automatic detection and classification of nuclei for cancer diagnosis impose a lot of challenges in developing state of the art algorithms due to the heterogeneity of cell nuclei and data set variability. Recently, a multitude of classification algorithms has used complex deep learning models for their dataset. However, most of these methods are rigid and their architectural arrangement suffers from inflexibility and non-interpretability. In this research article, we have proposed a hybrid and flexible deep learning architecture OLConvNet that integrates the interpretability of traditional object-level features and generalization of deep learning features by using a shallower Convolutional Neural Network (CNN) named as CNN_{3L}. CNN_{3L} reduces the training time by training fewer parameters and hence eliminating space constraints imposed by deeper algorithms. We used F1-score and multiclass Area Under the Curve (AUC) performance parameters to compare the results. To further strengthen the viability of our architectural approach, we tested our proposed methodology with state of the art deep learning architectures AlexNet, VGG16, VGG19, ResNet50, InceptionV3, and DenseNet121 as backbone networks. After a comprehensive analysis of classification results from all four architectures, we observed that our proposed model works well and perform better than contemporary complex algorithms.

The segmentation of cell nuclei in tissue images stained with the blood dye hematoxylin and eosin (H&E) is essential for various clinical applications and analyses. Due to the complex characteristics of cellular morphology, a large receptive field is considered crucial for generating high-quality segmentation. However, previous methods face challenges in achieving a balance between the receptive field and computational burden. To address this issue, we propose LKCell, a high-accuracy and efficient cell segmentation method. Its core insight lies in unleashing the potential of large convolution kernels to achieve computationally efficient large receptive fields. Specifically, (1) We transfer pre-trained large convolution kernel models to the medical domain for the first time, demonstrating their effectiveness in cell segmentation. (2) We analyze the redundancy of previous methods and design a new segmentation decoder based on large convolution kernels. It achieves higher performance while significantly reducing the number of parameters. We evaluate our method on the most challenging benchmark and achieve state-of-the-art results (0.5080 mPQ) in cell nuclei instance segmentation with only 21.6% FLOPs compared with the previous leading method. Our source code and models are available at https://github.com/hustvl/LKCell.

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.

With the rapid development of computational pathology, many AI-assisted diagnostic tasks have emerged. Cellular nuclei segmentation can segment various types of cells for downstream analysis, but it relies on predefined categories and lacks flexibility. Moreover, pathology visual question answering can perform image-level understanding but lacks region-level detection capability. To address this, we propose a new benchmark called Pathology Visual Grounding (PathVG), which aims to detect regions based on expressions with different attributes. To evaluate PathVG, we create a new dataset named RefPath which contains 27,610 images with 33,500 language-grounded boxes. Compared to visual grounding in other domains, PathVG presents pathological images at multi-scale and contains expressions with pathological knowledge. In the experimental study, we found that the biggest challenge was the implicit information underlying the pathological expressions. Based on this, we proposed Pathology Knowledge-enhanced Network (PKNet) as the baseline model for PathVG. PKNet leverages the knowledge-enhancement capabilities of Large Language Models (LLMs) to convert pathological terms with implicit information into explicit visual features, and fuses knowledge features with expression features through the designed Knowledge Fusion Module (KFM). The proposed method achieves state-of-the-art performance on the PathVG benchmark.

The classification of white blood cells (WBCs) from peripheral blood smears is critical for the diagnosis of leukemia. However, automated approaches still struggle due to challenges including class imbalance, domain shift, and morphological continuum confusion, where adjacent maturation stages exhibit subtle, overlapping features. We present a multi-stage fine-tuning methodology for 13-class WBC classification in the WBCBench 2026 Challenge (ISBI 2026). Our best-performing model is a fine-tuned DINOBloom-base, on which we train multiple classifier head families (linear, cosine, and multilayer perceptron (MLP)). The cosine head performed best on the mature granulocyte boundary (Band neutrophil (BNE) F1 = 0.470), the linear head on more immature granulocyte classes (Metamyelocyte (MMY) F1 = 0.585), and the MLP head on the most immature granulocyte (Promyelocyte (PMY) F1 = 0.733), revealing class-specific specialization. Based on this specialization, we construct a head-diverse ensemble, where the MLP head acts as the primary predictor, and its predictions within the four predefined confusion pairs are replaced only when two other head families agree. We further show that cases consistently misclassified by all models are substantially enriched for probable labeling errors or inherent morphological ambiguity.

We investigate the stellar shape and size-mass relationship of X-ray selected Active Galactic Nuclei (AGN) host galaxies using the high-angular resolution and deep sensitivity in the near-infrared of the COSMOS-Web JWST survey field. We present the rest-frame 1-mu m size, stellar mass, Sersic index, axis-ratio, Gini-M_{20} parameters of 690 moderate luminosity AGNs between redshift 0-3 and with stellar mass log M_ssim 10.75. We find that AGN host galaxies have an effective radius of 1-5 kpc, which is between star-forming (SFG) and quiescent galaxies (QGs) of the same stellar mass. AGN hosts have similar size-mass trends as SFG and QGs, being smaller at higher redshift for the same stellar mass. The slope of the size-mass relationship of AGN host galaxies is steeper than that of star-forming galaxies. Their rest-frame 1mu m stellar morphology indicates a significant spheroidal component. We observed a low merger fraction (6%) in our sample as well as substructures similar to disks, bars, and spiral arms in the residual images, which are in tension with evolutionary pathways that require major mergers. However, it may also be due to the different timescales between mergers and AGN activity.

Cell and nucleus segmentation are fundamental tasks for quantitative bioimage analysis. Despite progress in recent years, biologists and other domain experts still require novel algorithms to handle increasingly large and complex real-world datasets. These algorithms must not only achieve state-of-the-art accuracy, but also be optimized for efficiency, portability and user-friendliness. Here, we introduce InstanSeg: a novel embedding-based instance segmentation pipeline designed to identify cells and nuclei in microscopy images. Using six public cell segmentation datasets, we demonstrate that InstanSeg can significantly improve accuracy when compared to the most widely used alternative methods, while reducing the processing time by at least 60%. Furthermore, InstanSeg is designed to be fully serializable as TorchScript and supports GPU acceleration on a range of hardware. We provide an open-source implementation of InstanSeg in Python, in addition to a user-friendly, interactive QuPath extension for inference written in Java. Our code and pre-trained models are available at https://github.com/instanseg/instanseg .

We present a statistical analysis of the connections between galactic bars, star formation, and active galactic nucleus (AGN) activity using 33,201 disk galaxies (0.01 < z < 0.05) from DESI DR1 cross-matched with Galaxy Zoo DESI. Based on morphological classifications, we identify 3,508 strongly barred and 8,335 weakly barred systems. We find that barred galaxies exhibit a clear bimodal distribution in color-mass space: weak bars are preferentially found in bluer, lower-mass disks, whereas strong bars are more common in massive, redder systems. Strongly barred galaxies are on average more massive and metal-rich than unbarred systems. In addition, strong bars enhance central SFRs in low-mass galaxies but reduce sSFRs in massive systems, reflecting a dual role where bars initially trigger central star formation but eventually promote quenching by accelerating gas consumption. In terms of nuclear activity, barred galaxies display a higher incidence of AGN activity. The presence of a bar is also associated with an increased fraction of powerful AGN, with the highest proportions found in strongly barred systems. However, the correlations between AGN activity and detailed bar structural parameters are weak, suggesting that the link between bars and nuclear activity is indirect and regulated by multiple factors. Overall, our results support a scenario in which bars facilitate angular-momentum transport and gas inflow, thereby driving central star formation and fueling supermassive black hole accretion while operating alongside other processes that shape galaxy evolution.

We measure the broad impact of galaxy structure on galaxy formation by examining the ongoing star formation and integrated star formation history as revealed through the stellar masses of galaxies at z < 7 based on JWST CEERS data from the Extended Groth Strip (EGS). Using the morphological catalog of 3965 visually classified JWST galaxies from Ferreira et al. (2023), we investigate the evolution of stars, and when they form, as a function of morphological type as well as galaxies classified as passive and starburst through spectral energy distributions. Although disk galaxies dominate the structures of galaxies at z < 7, we find that these disks are in general either `passive', or on the main-sequence of star formation, and do not contain a large population of starburst galaxies. We also find no significant correlation between morphological type and the star formation rate or colours of galaxies at z < 7. In fact, we find that the morphologically classified `spheroids' tend to be blue and are not found to be predominately passive systems at z > 1.5. We also find that the stellar mass function for disk galaxies does not evolve significantly during this time, whereas other galaxy types, such as the peculiar population, evolve dramatically, declining at lower redshifts. This indicates that massive peculiars are more common at higher redshifts. We further find that up to z sim 7, the specific star formation rate (sSFR) does not vary with visual morphology, but strongly depends on stellar mass and internal galaxy mass density. This demonstrates that at early epochs galaxy assembly is a mass-driven, rather than a morphologically-driven, process. Quenching of star formation is therefore a mass-dominated process throughout the universe's history, likely due to the presence of supermassive black holes.

Image-based or morphological profiling is a rapidly expanding field wherein cells are "profiled" by extracting hundreds to thousands of unbiased, quantitative features from images of cells that have been perturbed by genetic or chemical perturbations. The Cell Painting assay is the most popular imaged-based profiling assay wherein six small-molecule dyes label eight cellular compartments and thousands of measurements are made, describing quantitative traits such as size, shape, intensity, and texture within the nucleus, cytoplasm, and whole cell (Cimini et al., 2023). We have created the Cell Painting Gallery, a publicly available collection of Cell Painting datasets, with granular dataset descriptions and access instructions. It is hosted by AWS on the Registry of Open Data (RODA). As of January 2024, the Cell Painting Gallery holds 656 terabytes (TB) of image and associated numerical data. It includes the largest publicly available Cell Painting dataset, in terms of perturbations tested (Joint Undertaking for Morphological Profiling or JUMP (Chandrasekaran et al., 2023)), along with many other canonical datasets using Cell Painting, close derivatives of Cell Painting (such as LipocyteProfiler (Laber et al., 2023) and Pooled Cell Painting (Ramezani et al., 2023)).

Quantifying the morphology of galaxies has been an important task in astrophysics to understand the formation and evolution of galaxies. In recent years, the data size has been dramatically increasing due to several on-going and upcoming surveys. Labeling and identifying interesting objects for further investigations has been explored by citizen science through the Galaxy Zoo Project and by machine learning in particular with the convolutional neural networks (CNNs). In this work, we explore the usage of Vision Transformer (ViT) for galaxy morphology classification for the first time. We show that ViT could reach competitive results compared with CNNs, and is specifically good at classifying smaller-sized and fainter galaxies. With this promising preliminary result, we believe the ViT network architecture can be an important tool for galaxy morphological classification for the next generation surveys. Our open source, is publicly available at https://github.com/sliao-mi-luku/Galaxy-Zoo-Classification

Accurate whole-cell and nuclear segmentation is essential for precision pathology and spatial omics, yet routine hematoxylin and eosin (H&E) staining provides limited cytoplasmic contrast, restricting analyses to nuclei. Multiplex immunofluorescence (mIF) facilitates precise whole-cell delineation but remains constrained by cost and accessibility. We introduce VitaminP, a cross-modal learning framework enabling whole cell segmentation from H&E images. By learning from paired H&E-mIF data, VitaminP transfers molecular boundary information from mIF to overcome cytoplasmic contrast in H&E, establishing cross-modal supervision as a general strategy for recovering missing biological structure. We train VitaminP on 14 public datasets covering 34 cancer types and over 7 million instances, integrating publicly available labels with extensive annotations generated in this study, forming one of the largest resources for segmentation. VitaminP outperforms four state-of-the-art methods and generalizes to unseen datasets, including an in-house dataset spanning 24 rare cancer types. We further developed VitaminPScope, an open-source platform providing an interface for scalable inference and enabling broad adoption.

Deep Neural Networks (DNNs) are generated by sequentially performing linear and non-linear processes. Using a combination of linear and non-linear procedures is critical for generating a sufficiently deep feature space. The majority of non-linear operators are derivations of activation functions or pooling functions. Mathematical morphology is a branch of mathematics that provides non-linear operators for a variety of image processing problems. We investigate the utility of integrating these operations in an end-to-end deep learning framework in this paper. DNNs are designed to acquire a realistic representation for a particular job. Morphological operators give topological descriptors that convey salient information about the shapes of objects depicted in images. We propose a method based on meta-learning to incorporate morphological operators into DNNs. The learned architecture demonstrates how our novel morphological operations significantly increase DNN performance on various tasks, including picture classification and edge detection.

Deep learning has achieved impressive results in nuclei segmentation, but the massive requirement for pixel-wise labels remains a significant challenge. To alleviate the annotation burden, existing methods generate pseudo masks for model training using point labels. However, the generated masks are inevitably different from the ground truth, and these dissimilarities are not handled reasonably during the network training, resulting in the subpar performance of the segmentation model. To tackle this issue, we propose a framework named DoNuSeg, enabling Dynamic pseudo label Optimization in point-supervised Nuclei Segmentation. Specifically, DoNuSeg takes advantage of class activation maps (CAMs) to adaptively capture regions with semantics similar to annotated points. To leverage semantic diversity in the hierarchical feature levels, we design a dynamic selection module to choose the optimal one among CAMs from different encoder blocks as pseudo masks. Meanwhile, a CAM-guided contrastive module is proposed to further enhance the accuracy of pseudo masks. In addition to exploiting the semantic information provided by CAMs, we consider location priors inherent to point labels, developing a task-decoupled structure for effectively differentiating nuclei. Extensive experiments demonstrate that DoNuSeg outperforms state-of-the-art point-supervised methods. The code is available at https://github.com/shinning0821/MICCAI24-DoNuSeg.

Accurate anatomical labeling and analysis of the pulmonary structure and its surrounding anatomy from thoracic CT is getting increasingly important for understanding the etilogy of abnormalities or supporting targetted therapy and early interventions. Whilst lung and airway cell atlases have been attempted, there is a lack of fine-grained morphological atlases that are clinically deployable. In this work, we introduce AirMorph, a robust, end-to-end deep learning pipeline enabling fully automatic and comprehensive airway anatomical labeling at lobar, segmental, and subsegmental resolutions that can be used to create digital atlases of the lung. Evaluated across large-scale multi-center datasets comprising diverse pulmonary conditions, the AirMorph consistently outperformed existing segmentation and labeling methods in terms of accuracy, topological consistency, and completeness. To simplify clinical interpretation, we further introduce a compact anatomical signature quantifying critical morphological airway features, including stenosis, ectasia, tortuosity, divergence, length, and complexity. When applied to various pulmonary diseases such as pulmonary fibrosis, emphysema, atelectasis, consolidation, and reticular opacities, it demonstrates strong discriminative power, revealing disease-specific morphological patterns with high interpretability and explainability. Additionally, AirMorph supports efficient automated branching pattern analysis, potentially enhancing bronchoscopic navigation planning and procedural safety, offering a valuable clinical tool for improved diagnosis, targeted treatment, and personalized patient care.

Forensic histopathology, essential for determining cause of death and disease diagnosis, is severely impeded by postmortem autolysis, i.e., an irreversible, stochastic degradation process that distorts tissue morphology and introduces diagnostic subjectivity, thereby underscoring the value of restoring autolyzed images to a diagnostically plausible, pre-autolysis state for improving objectivity in forensic practice. This restoration task is fundamentally challenging due to the large, non-deterministic morphological changes caused by autolysis and the infeasibility of pixel-wise paired data, which invalidates assumptions underlying supervised and cycle/structure-consistent unpaired translation methods. To address this, we formalize forensic histopathology autolysis restoration as a new task: under unpaired supervision, transform postmortem images with severe autolysis into diagnostically meaningful ``antemortem'' representations. We contribute AutoPath, the first homologous yet unpaired dataset for this problem, constructed by splitting specimens into adjacent tissue blocks---one processed immediately, the other exposed to induce autolysis---yielding nearly ten thousand 10times patches from 69 cases with varying liver conditions. We further frame the problem as a Schrödinger Bridge between the autolyzed and non-autolyzed distributions, offering a principled approach to modeling stochastic, severe morphological degradation. Critically, we demonstrate the misalignment of generic image-level generative metrics (e.g., FID) with diagnostic utility and propose a forensically grounded, slide-level diagnostic distribution consistency evaluation. Overall, this work establishes a reproducible benchmark (encompassing task definition, a real-world dataset, and an evaluation methodology) toward rigorous and practically meaningful progress in autolysis restoration for forensic pathology.

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.

Spatial transcriptomics can resolve gene expression at single-cell resolution, but it is costly, limited to targeted panels of a few hundred to a few thousand genes, and applicable to only a small number of samples. H&E imaging, by contrast, is cheap and collected routinely at scale. This makes predicting single-cell expression directly from morphology a practical way to bring molecular analysis to large tissue archives. We therefore present VOICE, a multimodal foundation model that predicts single-cell gene expression from H&E images using paired Xenium data. VOICE first aligns cell centered H&E morphology from a pathology foundation model with single-cell expression embeddings from a transcriptome foundation model, trained using contrastive learning over 23 million cells. Next it predicts expression through two branches. One branch directly regresses expression from morphology. The other branch retrieves measured expression from similar reference cells, recovering genes that do not have morphological signal. Because genes vary in morphological predictability, VOICE fuses the two branches with a per-gene weight. After training, VOICE generalizes to heldout patients, slides, and partially overlapping gene panels from Xenium, and it consistently outperforms prior single-cell expression prediction methods on seven metrics.

The ENDF-6 format, widely used worldwide for storing and disseminating nuclear data, is managed by the Cross Sections Evaluation Working Group (CSEWG) and fully documented in the ENDF-6 formats manual. This manual employs a combination of formal and natural language, introducing the possibility of ambiguity in certain parts of the format specification. To eliminate the possibility of ambiguity, this contribution proposes a generalization of the formal language used in the ENDF-6 formats manual, which is precisely defined in extended Backus-Naur form (EBNF). This formalization also offers several other advantages, notably reducing the complexity of creating and updating parsing and validation programs for ENDF-6 formatted files. Moreover, the availability of a formal description enables the automatic mapping of the low-level ENDF-6 representation, provided by a sequence of numbers, to a more human-friendly hierarchical representation with variable names. Demonstrating these advantages, almost the entire ENDF-6 format description has been translated into the proposed formal language, accompanied by a reference implementation of a parser/translator. This implementation leverages the formal format specification to enable reading, writing, and validating ENDF-6 formatted files.

Earlier diagnosis of Leukemia can save thousands of lives annually. The prognosis of leukemia is challenging without the morphological information of White Blood Cells (WBC) and relies on the accessibility of expensive microscopes and the availability of hematologists to analyze Peripheral Blood Samples (PBS). Deep Learning based methods can be employed to assist hematologists. However, these algorithms require a large amount of labeled data, which is not readily available. To overcome this limitation, we have acquired a realistic, generalized, and large dataset. To collect this comprehensive dataset for real-world applications, two microscopes from two different cost spectrums (high-cost HCM and low-cost LCM) are used for dataset capturing at three magnifications (100x, 40x, 10x) through different sensors (high-end camera for HCM, middle-level camera for LCM and mobile-phone camera for both). The high-sensor camera is 47 times more expensive than the middle-level camera and HCM is 17 times more expensive than LCM. In this collection, using HCM at high resolution (100x), experienced hematologists annotated 10.3k WBC types (14) and artifacts, having 55k morphological labels (Cell Size, Nuclear Chromatin, Nuclear Shape, etc.) from 2.4k images of several PBS leukemia patients. Later on, these annotations are transferred to other 2 magnifications of HCM, and 3 magnifications of LCM, and on each camera captured images. Along with the LeukemiaAttri dataset, we provide baselines over multiple object detectors and Unsupervised Domain Adaptation (UDA) strategies, along with morphological information-based attribute prediction. The dataset will be publicly available after publication to facilitate the research in this direction.

Tissue phenotyping is a fundamental task in learning objective characterizations of histopathologic biomarkers within the tumor-immune microenvironment in cancer pathology. However, whole-slide imaging (WSI) is a complex computer vision in which: 1) WSIs have enormous image resolutions with precludes large-scale pixel-level efforts in data curation, and 2) diversity of morphological phenotypes results in inter- and intra-observer variability in tissue labeling. To address these limitations, current efforts have proposed using pretrained image encoders (transfer learning from ImageNet, self-supervised pretraining) in extracting morphological features from pathology, but have not been extensively validated. In this work, we conduct a search for good representations in pathology by training a variety of self-supervised models with validation on a variety of weakly-supervised and patch-level tasks. Our key finding is in discovering that Vision Transformers using DINO-based knowledge distillation are able to learn data-efficient and interpretable features in histology images wherein the different attention heads learn distinct morphological phenotypes. We make evaluation code and pretrained weights publicly-available at: https://github.com/Richarizardd/Self-Supervised-ViT-Path.

We present Singpath-VL, a vision-language large model, to fill the vacancy of AI assistant in cervical cytology. Recent advances in multi-modal large language models (MLLMs) have significantly propelled the field of computational pathology. However, their application in cytopathology, particularly cervical cytology, remains underexplored, primarily due to the scarcity of large-scale, high-quality annotated datasets. To bridge this gap, we first develop a novel three-stage pipeline to synthesize a million-scale image-description dataset. The pipeline leverages multiple general-purpose MLLMs as weak annotators, refines their outputs through consensus fusion and expert knowledge injection, and produces high-fidelity descriptions of cell morphology. Using this dataset, we then fine-tune the Qwen3-VL-4B model via a multi-stage strategy to create a specialized cytopathology MLLM. The resulting model, named Singpath-VL, demonstrates superior performance in fine-grained morphological perception and cell-level diagnostic classification. To advance the field, we will open-source a portion of the synthetic dataset and benchmark.

Understanding how cellular morphology, gene expression, and spatial context jointly shape tissue function is a central challenge in biology. Image-based spatial transcriptomics technologies now provide high-resolution measurements of cell images and gene expression profiles, but existing methods typically analyze these modalities in isolation or at limited resolution. We address the problem by introducing SPATIA, a multi-level generative and predictive model that learns unified, spatially aware representations by fusing morphology, gene expression, and spatial context from the cell to the tissue level. SPATIA also incorporates a spatially conditioned generative framework with confidence-aware OT reweighting and morphology-profile alignment for modeling target-state morphology distributions. Specifically, we propose a confidence-aware flow matching objective that reweights weak optimal-transport pairs based on uncertainty. We further apply morphology-profile alignment to encourage biologically meaningful image generation, enabling the modeling of microenvironment-dependent phenotypic transitions. We assembled a multi-scale dataset consisting of 25.9 million cell-gene pairs across 17 tissues. We benchmark SPATIA against 18 models across 12 tasks, spanning categories such as phenotype generation, annotation, clustering, gene imputation, and cross-modal prediction. SPATIA achieves improved performance over state-of-the-art models, improving generative fidelity by 8% and predictive accuracy by up to 3%.

Representation learning of pathology whole-slide images (WSIs) has been has primarily relied on weak supervision with Multiple Instance Learning (MIL). However, the slide representations resulting from this approach are highly tailored to specific clinical tasks, which limits their expressivity and generalization, particularly in scenarios with limited data. Instead, we hypothesize that morphological redundancy in tissue can be leveraged to build a task-agnostic slide representation in an unsupervised fashion. To this end, we introduce PANTHER, a prototype-based approach rooted in the Gaussian mixture model that summarizes the set of WSI patches into a much smaller set of morphological prototypes. Specifically, each patch is assumed to have been generated from a mixture distribution, where each mixture component represents a morphological exemplar. Utilizing the estimated mixture parameters, we then construct a compact slide representation that can be readily used for a wide range of downstream tasks. By performing an extensive evaluation of PANTHER on subtyping and survival tasks using 13 datasets, we show that 1) PANTHER outperforms or is on par with supervised MIL baselines and 2) the analysis of morphological prototypes brings new qualitative and quantitative insights into model interpretability.

Pathology Foundation Models (FMs) have shown strong performance across a wide range of pathology image representation and diagnostic tasks. However, FMs do not exhibit the expected performance advantage over traditional specialized models in Nuclei Detection and Classification (NDC). In this work, we reveal that jointly optimizing nuclei detection and classification leads to severe representation degradation in FMs. Moreover, we identify that the substantial intrinsic disparity in task difficulty between nuclei detection and nuclei classification renders joint NDC optimization unnecessarily computationally burdensome for the detection stage. To address these challenges, we propose DeNuC, a simple yet effective method designed to break through existing bottlenecks by Decoupling Nuclei detection and Classification. DeNuC employs a lightweight model for accurate nuclei localization, subsequently leveraging a pathology FM to encode input images and query nucleus-specific features based on the detected coordinates for classification. Extensive experiments on three widely used benchmarks demonstrate that DeNuC effectively unlocks the representational potential of FMs for NDC and significantly outperforms state-of-the-art methods. Notably, DeNuC improves F1 scores by 4.2% and 3.6% (or higher) on the BRCAM2C and PUMA datasets, respectively, while using only 16% (or fewer) trainable parameters compared to other methods. Code is available at https://github.com/ZijiangY1116/DeNuC.

This article presents a review about the main CERN n\_TOF contributions to the field of neutron-capture experiments of interest for s-process nucleosynthesis studies over the last 25 years, with special focus on the measurement of radioactive isotopes. A few recent capture experiments on stable isotopes of astrophysical interest are also discussed. Results on s-process branching nuclei are appropriate to illustrate how advances in detection systems and upgrades in the facility have enabled increasingly challenging experiments and, as a consequence, have led to a better understanding and modeling of the s-process mechanism of nucleosynthesis. New endeavors combining radioactive-ion beams from ISOLDE for the production of radioisotopically pure samples for activation experiments at the new NEAR facility at n\_TOF are briefly discussed. On the basis of these new exciting results, also current limitations of state-of-the-art TOF and activation techniques will be depicted, thereby showing the pressing need for further upgrades and enhancements on both facilities and detection systems. A brief account of the potential technique based on inverse kinematics for direct neutron-capture measurements is also presented.

Mitotic figures are classified into typical and atypical variants, with atypical counts correlating strongly with tumor aggressiveness. Accurate differentiation is therefore essential for patient prognostication and resource allocation, yet remains challenging even for expert pathologists. Here, we leveraged Pathology Foundation Models (PFMs) pre-trained on large histopathology datasets and applied parameter-efficient fine-tuning via low-rank adaptation. In addition, we incorporated ConvNeXt V2, a state-of-the-art convolutional neural network architecture, to complement PFMs. During training, we employed a fisheye transform to emphasize mitoses and Fourier Domain Adaptation using ImageNet target images. Finally, we ensembled multiple PFMs to integrate complementary morphological insights, achieving competitive balanced accuracy on the Preliminary Evaluation Phase dataset.

The extended kernel ridge regression (EKRR) method with odd-even effects was adopted to improve the description of the nuclear charge radius using five commonly used nuclear models. These are: (i) the isospin dependent A^{1/3} formula, (ii) relativistic continuum Hartree-Bogoliubov (RCHB) theory, (iii) Hartree-Fock-Bogoliubov (HFB) model HFB25, (iv) the Weizs\"acker-Skyrme (WS) model WS^ast, and (v) HFB25^ast model. In the last two models, the charge radii were calculated using a five-parameter formula with the nuclear shell corrections and deformations obtained from the WS and HFB25 models, respectively. For each model, the resultant root-mean-square deviation for the 1014 nuclei with proton number Z geq 8 can be significantly reduced to 0.009-0.013~fm after considering the modification with the EKRR method. The best among them was the RCHB model, with a root-mean-square deviation of 0.0092~fm. The extrapolation abilities of the KRR and EKRR methods for the neutron-rich region were examined and it was found that after considering the odd-even effects, the extrapolation power was improved compared with that of the original KRR method. The strong odd-even staggering of nuclear charge radii of Ca and Cu isotopes and the abrupt kinks across the neutron N=126 and 82 shell closures were also calculated and could be reproduced quite well by calculations using the EKRR method.

Cytopathology detection requires open-vocabulary recognition because cellular categories are fine-grained, long-tailed, and continuously evolving across different organ systems. However, existing cytology detectors are mostly single-domain and closed-set, and there is still no unified benchmark for evaluating open-vocabulary cytopathology detection. We present PentaCyto, a multi-domain benchmark covering cervical, urinary, respiratory, serous fluid, and thyroid cytology, with 24 base categories and 9 held-out novel categories. Each category is associated with structured cytomorphology prompts that describe diagnostic morphological attributes and provide clinically grounded textual knowledge. We further propose CytoSPM, an efficient detector based on a decoupled two-stage design. It first extracts reusable class-agnostic visual representations, and then performs class-aware structural prompt matching with class names and cytomorphology prompts. On PentaCyto, CytoSPM outperforms existing methods in novel-category detection and open-vocabulary detection while maintaining efficient inference.

During developmental processes such as embryogenesis, how a group of cells fold into specific structures, is a central question in biology that defines how living organisms form. Establishing tissue-level morphology critically relies on how every single cell decides to position itself relative to its neighboring cells. Despite its importance, it remains a major challenge to understand and predict the behavior of every cell within the living tissue over time during such intricate processes. To tackle this question, we propose a geometric deep learning model that can predict multicellular folding and embryogenesis, accurately capturing the highly convoluted spatial interactions among cells. We demonstrate that multicellular data can be represented with both granular and foam-like physical pictures through a unified graph data structure, considering both cellular interactions and cell junction networks. We successfully use our model to achieve two important tasks, interpretable 4-D morphological sequence alignment, and predicting local cell rearrangements before they occur at single-cell resolution. Furthermore, using an activation map and ablation studies, we demonstrate that cell geometries and cell junction networks together regulate local cell rearrangement which is critical for embryo morphogenesis. This approach provides a novel paradigm to study morphogenesis, highlighting a unified data structure and harnessing the power of geometric deep learning to accurately model the mechanisms and behaviors of cells during development. It offers a pathway toward creating a unified dynamic morphological atlas for a variety of developmental processes such as embryogenesis.

Next generations of radio surveys are expected to identify tens of millions of new sources, and identifying and classifying their morphologies will require novel and more efficient methods. Self-Organising Maps (SOMs), a type of unsupervised machine learning, can be used to address this problem. We map 251,259 multi-Gaussian sources from Rapid ASKAP Continuum Survey (RACS) onto a SOM with discrete neurons. Similarity metrics, such as Euclidean distances, can be used to identify the best-matching neuron or unit (BMU) for each input image. We establish a reliability threshold by visually inspecting a subset of input images and their corresponding BMU. We label the individual neurons based on observed morphologies and these labels are included in our value-added catalogue of RACS sources. Sources for which the Euclidean distance to their BMU is lesssim 5 (accounting for approximately 79% of sources) have an estimated >90% reliability for their SOM-derived morphological labels. This reliability falls to less than 70% at Euclidean distances gtrsim 7. Beyond this threshold it is unlikely that the morphological label will accurately describe a given source. Our catalogue of complex radio sources from RACS with their SOM-derived morphological labels from this work will be made publicly available.

In this work we update the L-Galaxies semi-analytic model (SAM) to better follow the physical processes responsible for the growth of bulges via disc instabilities (leading to pseudo-bulges) and mergers (leading to classical bulges). We address the former by considering the contribution of both stellar and gaseous discs in the stability of the galaxy, and we update the latter by including dissipation of energy in gas-rich mergers. Furthermore, we introduce angular momentum losses during cooling and find that an accurate match to the observed correlation between stellar disc scale length and mass at z ~ 0.0 requires that the gas loses 20% of its initial specific angular momentum to the corresponding dark matter halo during the formation of the cold gas disc. We reproduce the observed trends between the stellar mass and specific angular momentum for both disc- and bulge-dominated galaxies, with the former rotating faster than the latter of the same mass. We conclude that a two-component instability recipe provides a morphologically diverse galaxy sample which matches the observed fractional breakdown of galaxies into different morphological types. This recipe also enables us to obtain an excellent fit to the morphology-mass relation and stellar mass function of different galactic types. Finally, we find that energy dissipation during mergers reduces the merger remnant sizes and allows us to match the observed mass-size relation for bulge-dominated systems.

Computational pathology can lead to saving human lives, but models are annotation hungry and pathology images are notoriously expensive to annotate. Self-supervised learning has shown to be an effective method for utilizing unlabeled data, and its application to pathology could greatly benefit its downstream tasks. Yet, there are no principled studies that compare SSL methods and discuss how to adapt them for pathology. To address this need, we execute the largest-scale study of SSL pre-training on pathology image data, to date. Our study is conducted using 4 representative SSL methods on diverse downstream tasks. We establish that large-scale domain-aligned pre-training in pathology consistently out-performs ImageNet pre-training in standard SSL settings such as linear and fine-tuning evaluations, as well as in low-label regimes. Moreover, we propose a set of domain-specific techniques that we experimentally show leads to a performance boost. Lastly, for the first time, we apply SSL to the challenging task of nuclei instance segmentation and show large and consistent performance improvements under diverse settings.

In the last ten years, Convolutional Neural Networks (CNNs) have formed the basis of deep-learning architectures for most computer vision tasks. However, they are not necessarily optimal. For example, mathematical morphology is known to be better suited to deal with binary images. In this work, we create a morphological neural network that handles binary inputs and outputs. We propose their construction inspired by CNNs to formulate layers adapted to such images by replacing convolutions with erosions and dilations. We give explainable theoretical results on whether or not the resulting learned networks are indeed morphological operators. We present promising experimental results designed to learn basic binary operators, and we have made our code publicly available online.

The science of fractography revolves around the correlation between topographic characteristics of the fracture surface and the mechanisms and external conditions leading to their creation. While being a topic of investigation for centuries, it has remained mostly qualitative to date. A quantitative analysis of fracture surfaces is of prime interest for both the scientific community and the industrial sector, bearing the potential for improved understanding on the mechanisms controlling the fracture process and at the same time assessing the reliability of computational models currently being used for material design. With new advances in the field of image analysis, and specifically with machine learning tools becoming more accessible and reliable, it is now feasible to automate the process of extracting meaningful information from fracture surface images. Here, we propose a method of identifying and quantifying the relative appearance of intergranular and transgranular fracture events from scanning electron microscope images. The newly proposed method is based on a convolutional neural network algorithm for semantic segmentation. The proposed method is extensively tested and evaluated against two ceramic material systems (Al_2O_3,MgAl_2O_4) and shows high prediction accuracy, despite being trained on only one material system (MgAl_2O_4). While here attention is focused on brittle fracture characteristics, the method can be easily extended to account for other fracture morphologies, such as dimples, fatigue striations, etc.

Low-mass X-ray binaries with a neutron star as the primary object show a complex array of phenomenology during outbursts. The observed variability in X-ray emission primarily arises from changes in the innermost regions of the accretion disk, neutron star surface, and corona. In this work, we present the results of a comprehensive X-ray spectral and timing analysis of the neutron star transient MAXI J1807+132 during its 2023 outburst using data from the NICER observatory. The outburst is marked by a very rapid rise in the count rate by about a factor of 20 in a day. The source undergoes full state transitions and displays hysteresis effect in the hardness and rms intensity diagrams. Spectral analysis with a three-component model is consistent with disk truncation during the hard states and reaching the last stable orbit during the intermediate and soft states. We discuss the different values of the last stable radius in the context of possible distance of the source and magnetic field strength. The characteristic frequencies throughout the hard and intermediate states are found to be strongly correlated with the inner radius of the disk. Together with the spectral and fast variability properties, we attempt to trace the evolution of the size of the corona along the outburst. Following the main outburst, the source undergoes a high amplitude reflare wherein it shows a complex behavior with relatively high variability (10 %), but low hardness.

We present 5 GHz e-MERLIN radio images at 50 mas resolution of the nuclear regions of the Legacy e-MERLIN Multi-band Imaging of Nearby Galaxies survey (LeMMINGs), the deepest statistically complete radio-band survey of the local Universe (<120 Mpc), consisting of 280 galaxies spanning all morphological and nuclear types. We detect nuclear radio emission above a median 5 sigma threshold of 0.33 mJy beam^-1 in 68 of 280 sources (24 percent), with core luminosities in the range 10^35 to 10^41.9 erg s^-1. The radio emission is attributed to active galactic nuclei, circumnuclear star formation, or, in the case of NGC 3690, a tidal disruption event. The brightest radio nuclei, with brightness temperatures >=10^6 K, reside in optically active galaxies such as LINERs and Seyferts. The detection rate for inactive systems (H II and absorption-line galaxies), which may host low-luminosity active galactic nuclei, is 8 percent. Most detections (78 percent) are compact (<10 pc), while the remaining 22 percent show extended jet-like features up to 380 pc. Compared to the 1.5 GHz LeMMINGs data, the 5 GHz observations provide superior resolution and spatial filtering, resolving out large-scale structures and isolating genuine nuclear emission. Our results suggest that low-luminosity active galactic nuclei are the primary manifestation of black hole activity in the local Universe in the form of compact jets and cores, with a preference for early-type hosts. The two LeMMINGs campaigns indicate that up to 30 percent of the local galaxy population hosts a radio-active nucleus, highlighting the necessity of high-resolution, high-sensitivity imaging for uncovering nuclear emission at the lowest luminosities.

Bars are important drivers of galaxy evolution, influencing many physical processes and properties. Characterising bars is a difficult task, especially in large-scale surveys. In this work, we propose a novel morphological segmentation technique for determining bar lengths based on deep learning. We develop U-Nets capable of decomposing galaxy images into pixel masks highlighting the regions corresponding to bars and spiral arms. We demonstrate the versatility of this technique through applying our models to galaxy images from two different observational datasets with different source imagery, and to RGB colour and monochromatic galaxy imaging. We apply our models to analyse SDSS and Subaru HSC imaging of barred galaxies from the NA10 and SAMI catalogues in order to determine the dependence of bar length on stellar mass, morphology, redshift and the spin parameter proxy λ_{R_e}. Based on the predicted bar masks, we show that the relative bar scale length varies with morphology, with early type galaxies hosting longer bars. While bars are longer in more massive galaxies in absolute terms, relative to the galaxy disc they are actually shorter. We also find that the normalised bar length decreases with increasing redshift, with bars in early-type galaxies exhibiting the strongest rate of decline. We show that it is possible to distinguish spiral arms and bars in monochrome imaging, although for a given galaxy the estimated length in monochrome tends to be longer than in colour imaging. Our morphological segmentation technique can be efficiently applied to study bars in large-scale surveys and even in cosmological simulations.

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.

The catalog of ringed galaxies was compiled through visual classification of synthetic images from the TNG50 simulation. Galaxies were selected based on specific criteria: a redshift range of 0.01 < z < 0.1, stellar mass M_star >10^9 M_odot, stellar half-mass radius r_{50} > 1 kpc, and specific star formation rate (sSFR), log(sSFR/yr^{-1}) > -13. Our classification allowed for differentiation between inner rings, outer rings, combinations of rings, and partial rings (pseudo-rings), including barred and non-barred ringed galaxies. We constructed a control sample of non-ringed galaxies with similar redshift, stellar mass, and environmental density distributions. We identified 807 ringed galaxies. Approximately 59% possess an inner ring, 22% a partial ring, 12% an outer ring, and 7% have i+o rings. Our statistical analysis reveals that 64% (507 galaxies) exhibit bars. Ringed galaxies exhibit lower efficiency for star formation, reduced gas fractions, redder colors, and higher metallicities compared to non-ringed disk objects. They also show greater variability in metallicity for a given stellar mass. From the analysis of radial profiles, galaxies with outer rings exhibit a r_{50} similar to or slightly larger than their control group, while those with inner or partial rings tend to have smaller sizes. A deeper exploration of radial density profiles revealed a pronounced central mass deficit preceding the ring structures, with inner and outer rings located at r_{50} and 1.5 , r_{50}, respectively. Galaxies with both i+o rings have inner rings that are more compact and massive. Additionally, galaxies with partial rings exhibit deeper mass profiles than their controls, particularly in central areas. These findings improve our understanding of galactic evolution and the complex interplay between mass distribution and morphology.

High-content screening (HCS) assays based on high-throughput microscopy techniques such as Cell Painting have enabled the interrogation of cells' morphological responses to perturbations at an unprecedented scale. The collection of such data promises to facilitate a better understanding of the relationships between different perturbations and their effects on cellular state. Towards achieving this goal, recent advances in cross-modal contrastive learning could, in theory, be leveraged to learn a unified latent space that aligns perturbations with their corresponding morphological effects. However, the application of such methods to HCS data is not straightforward due to substantial differences in the semantics of Cell Painting images compared to natural images, and the difficulty of representing different classes of perturbations (e.g., small molecule vs CRISPR gene knockout) in a single latent space. In response to these challenges, here we introduce CellCLIP, a cross-modal contrastive learning framework for HCS data. CellCLIP leverages pre-trained image encoders coupled with a novel channel encoding scheme to better capture relationships between different microscopy channels in image embeddings, along with natural language encoders for representing perturbations. Our framework outperforms current open-source models, demonstrating the best performance in both cross-modal retrieval and biologically meaningful downstream tasks while also achieving significant reductions in computation time.

High-content cellular imaging, transcriptomics, and proteomics data provide rich and complementary views on the molecular layers of biology that influence cellular states and function. However, the biological determinants through which changes in multi-omics measurements influence cellular morphology have not yet been systematically explored, and the degree to which cell imaging could potentially enable the prediction of multi-omics directly from cell imaging data is therefore currently unclear. Here, we address the question of whether it is possible to predict bulk multi-omics measurements directly from cell images using Image2Omics - a deep learning approach that predicts multi-omics in a cell population directly from high-content images of cells stained with multiplexed fluorescent dyes. We perform an experimental evaluation in gene-edited macrophages derived from human induced pluripotent stem cells (hiPSC) under multiple stimulation conditions and demonstrate that Image2Omics achieves significantly better performance in predicting transcriptomics and proteomics measurements directly from cell images than predictions based on the mean observed training set abundance. We observed significant predictability of abundances for 4927 (18.72%; 95% CI: 6.52%, 35.52%) and 3521 (13.38%; 95% CI: 4.10%, 32.21%) transcripts out of 26137 in M1 and M2-stimulated macrophages respectively and for 422 (8.46%; 95% CI: 0.58%, 25.83%) and 697 (13.98%; 95% CI: 2.41%, 32.83%) proteins out of 4986 in M1 and M2-stimulated macrophages respectively. Our results show that some transcript and protein abundances are predictable from cell imaging and that cell imaging may potentially, in some settings and depending on the mechanisms of interest and desired performance threshold, even be a scalable and resource-efficient substitute for multi-omics measurements.

We describe pre-perihelion optical observations of interstellar comet 3I/ATLAS taken during July - September 2025 using the Nordic Optical Telescope. Fixed aperture photometry of the comet is well described by a power law function of heliocentric distance, rH, with the exponent (``index") n = 3.8+/-0.3 across the 4.6 au to 1.8 au distance range (phase function 0.04+/-0.02 magnitude/degree assumed). This indicates that the dust production rates vary in proportion to rH**(-1.8+/-0.3). An rH**(-2) variation is expected of a strongly volatile material, and consistent with independent spectroscopic observations showing that carbon dioxide is the primary driver of activity. The measured heliocentric index is unremarkable in the context of solar system comets, for which n is widely dispersed, and provides no basis on which to describe 3I as either dynamically old (thermally processed) or new (pristine). The morphology of the comet changes from a Sun-facing dust fan in the early 2025 July observations, to one dominated by an antisolar dust tail at later dates. We attribute the delayed emergence of the tail to the large size (effective radius 0.1 mm) and slow ejection (5 m/s) of the optically dominant dust particles, and their consequently sluggish response to solar radiation pressure. Small (micron-sized) particles may be present but not in numbers sufficient to dominate the scattering cross-section. Their relative depletion possibly reflects interparticle cohesion, which binds small particles more effectively than large ones. A similar preponderance of 0.1 mm grains was reported in 2I/Borisov. However, 2I differed from 3I in having a much smaller (asteroid-like) heliocentric index, n = 1.9+/-0.1. Dust production rates in 3I are 180 kg/s at 2 au, compared with 70 kg/s in 2I/Borisov at the same distance.

Tissue segmentation is a routine preprocessing step to reduce the computational cost of whole slide image (WSI) analysis by excluding background regions. Traditional image processing techniques are commonly used for tissue segmentation, but often require manual adjustments to parameter values for atypical cases, fail to exclude all slide and scanning artifacts from the background, and are unable to segment adipose tissue. Pen marking artifacts in particular can be a potential source of bias for subsequent analyses if not removed. In addition, several applications require the separation of individual cross-sections, which can be challenging due to tissue fragmentation and adjacent positioning. To address these problems, we develop a convolutional neural network for tissue and pen marking segmentation using a dataset of 200 H&E stained WSIs. For separating tissue cross-sections, we propose a novel post-processing method based on clustering predicted centroid locations of the cross-sections in a 2D histogram. On an independent test set, the model achieved a mean Dice score of 0.981pm0.033 for tissue segmentation and a mean Dice score of 0.912pm0.090 for pen marking segmentation. The mean absolute difference between the number of annotated and separated cross-sections was 0.075pm0.350. Our results demonstrate that the proposed model can accurately segment H&E stained tissue cross-sections and pen markings in WSIs while being robust to many common slide and scanning artifacts. The model with trained model parameters and post-processing method are made publicly available as a Python package called SlideSegmenter.

We present an extension of the publicly available Spinal-Multiple-Myeloma-SEG dataset, a dual-energy CT imaging resource for multiple myeloma research. The purpose of this dataset is to enable voxel-wise analysis of vertebral bone microstructure by adding expert-validated segmentation of the trabecular compartment of lumbar vertebrae. The dataset consists of 72 dual-energy CT examinations from 67 adult patients (mean age 66 years, range 48--85; 36\% female), acquired retrospectively using a dual-layer dual-energy CT system. It includes conventional CT, virtual monoenergetic images, and calcium-suppressed reconstructions, along with structured clinical metadata. The data are provided in DICOM format, while segmentation masks are available in both NIfTI and DICOM-SEG formats. The primary intended applications include trabecular bone segmentation, quantitative bone mineral density-related analysis, and development of deep learning models for vertebral anatomy and disease-affected bone structures in multiple myeloma. The dataset supports both segmentation and multimodal learning tasks in pathological and non-pathological bone. Initial trabecular segmentation masks were generated using a pretrained nnU-Net model and subsequently refined through manual expert correction and radiological quality control, ensuring anatomical consistency. The original dataset is publicly available via TCIA (https://doi.org/10.7937/k4qv-hh78{https://doi.org/10.7937/k4qv-hh78}), while the trabecular segmentation extension (Version 2) is released through Zenodo (https://doi.org/10.5281/zenodo.21628232{https://doi.org/10.5281/zenodo.21628232}) under the CC BY 4.0 license. The Zenodo release provides immediate public access to the segmentation masks and will be additionally incorporated into the official TCIA collection after completion of the curation process.

We develop a learning framework for building deformable templates, which play a fundamental role in many image analysis and computational anatomy tasks. Conventional methods for template creation and image alignment to the template have undergone decades of rich technical development. In these frameworks, templates are constructed using an iterative process of template estimation and alignment, which is often computationally very expensive. Due in part to this shortcoming, most methods compute a single template for the entire population of images, or a few templates for specific sub-groups of the data. In this work, we present a probabilistic model and efficient learning strategy that yields either universal or conditional templates, jointly with a neural network that provides efficient alignment of the images to these templates. We demonstrate the usefulness of this method on a variety of domains, with a special focus on neuroimaging. This is particularly useful for clinical applications where a pre-existing template does not exist, or creating a new one with traditional methods can be prohibitively expensive. Our code and atlases are available online as part of the VoxelMorph library at http://voxelmorph.csail.mit.edu.

Extracting single-cell information from microscopy data requires accurate instance-wise segmentations. Obtaining pixel-wise segmentations from microscopy imagery remains a challenging task, especially with the added complexity of microstructured environments. This paper presents a novel dataset for segmenting yeast cells in microstructures. We offer pixel-wise instance segmentation labels for both cells and trap microstructures. In total, we release 493 densely annotated microscopy images. To facilitate a unified comparison between novel segmentation algorithms, we propose a standardized evaluation strategy for our dataset. The aim of the dataset and evaluation strategy is to facilitate the development of new cell segmentation approaches. The dataset is publicly available at https://christophreich1996.github.io/yeast_in_microstructures_dataset/ .

Large-scale cell microscopy screens are used in drug discovery and molecular biology research to study the effects of millions of chemical and genetic perturbations on cells. To use these images in downstream analysis, we need models that can map each image into a feature space that represents diverse biological phenotypes consistently, in the sense that perturbations with similar biological effects have similar representations. In this work, we present the largest foundation model for cell microscopy data to date, a new 1.9 billion-parameter ViT-G/8 MAE trained on over 8 billion microscopy image crops. Compared to a previous published ViT-L/8 MAE, our new model achieves a 60% improvement in linear separability of genetic perturbations and obtains the best overall performance on whole-genome biological relationship recall and replicate consistency benchmarks. Beyond scaling, we developed two key methods that improve performance: (1) training on a curated and diverse dataset; and, (2) using biologically motivated linear probing tasks to search across each transformer block for the best candidate representation of whole-genome screens. We find that many self-supervised vision transformers, pretrained on either natural or microscopy images, yield significantly more biologically meaningful representations of microscopy images in their intermediate blocks than in their typically used final blocks. More broadly, our approach and results provide insights toward a general strategy for successfully building foundation models for large-scale biological data.

Polyploidization is an important evolutionary process which affects organisms ranging from plants to fish and fungi. The signal left behind by it is in the form of a species' ploidy level (number of complete chromosome sets found in a cell) which is inherently non-treelike. Currently available tools for reconstructing the evolutionary past of a polyploid dataset generally start with a multi-labelled tree obtained for a dataset of interest and then derive a (phylogenetic) network from that tree in some way that reflects that past by interpreting the networks's vertices of indegree at least two as polyploidization events. Since obtaining such a tree can be computationally expensive it is paramount to have alternative approaches available that allow one to shed light into the reticulate evolutionary past of a polyploid dataset. SPRINT aims to reconstruct the evolutionary past of a polyploid dataset in terms of a binary network which realises the dataset's ploidy profile (vector of ploidy levels of the dataset's taxa) and requires the fewest number of polyploidization events. It does this by representing the ploidy level of a species x in terms of the number of directed paths from the root of the network to the leaf of the network labelled by x. SPRINT is distributed on GitHub: https://github.com/lmaher1/SPRINT.

The stellar structures of star-forming galaxies (SFGs) undergo significant size growth during their mass assembly and must pass through a compaction phase as they evolve into quiescent galaxies (QGs). To shed light on the mechanisms behind this structural evolution, we study the morphology of the star-forming components of 665 SFGs at 0<z<2.5 measured using JWST/MIRI observation and compare them with the morphology of their stellar components taken from the literature. The stellar and star-forming components of most SFGs (66%) have extended disk-like structures that are aligned with each other and are of the same size. The star-forming components of these galaxies follow a mass-size relation, similar to that followed by their stellar components. At the highest mass, the optical S\'ersic index of these SFGs increases to 2.5, suggesting the presence of a dominant stellar bulge. Because their star-forming components remain disk-like, these bulges cannot have formed by secular in-situ growth. We identify a second population of galaxies lying below the MIR mass-size relation, with compact star-forming components embedded in extended stellar components (EC galaxy). These galaxies are overall rare (15%) but become more dominant (30%) at high mass (>10^{10.5}M_odot). The compact star-forming components of these galaxies are also concentrated and slightly spheroidal, suggesting that this compaction phase can build dense bulge in-situ. Finally, we identify a third population of SFGs (19%), with both compact stellar and star-forming components. The density of their stellar cores resemble those of QGs and are compatible with being the descendants of EC galaxy. Overall, the structural evolution of SFGs is mainly dominated by a secular inside-out growth, which can, however, be interrupted by violent compaction phase(s) that can build dominant stellar bulges like those in massive SFGs or QGs.

Nasal Cytology is a new and efficient clinical technique to diagnose rhinitis and allergies that is not much widespread due to the time-consuming nature of cell counting; that is why AI-aided counting could be a turning point for the diffusion of this technique. In this article we present the first dataset of rhino-cytological field images: the NCD (Nasal Cytology Dataset), aimed to train and deploy Object Detection models to support physicians and biologists during clinical practice. The real distribution of the cytotypes, populating the nasal mucosa has been replicated, sampling images from slides of clinical patients, and manually annotating each cell found on them. The correspondent object detection task presents non'trivial issues associated with the strong class imbalancement, involving the rarest cell types. This work contributes to some of open challenges by presenting a novel machine learning-based approach to aid the automated detection and classification of nasal mucosa cells: the DETR and YOLO models shown good performance in detecting cells and classifying them correctly, revealing great potential to accelerate the work of rhinology experts.

In this work, we update the unsupervised machine learning (UML) step by proposing an algorithm based on ConvNeXt large model coding to improve the efficiency of unlabeled galaxy morphology classifications. The method can be summarized into three key aspects as follows: (1) a convolutional autoencoder is used for image denoising and reconstruction and the rotational invariance of the model is improved by polar coordinate extension; (2) utilizing a pre-trained convolutional neural network (CNN) named ConvNeXt for encoding the image data. The features were further compressed via a principal component analysis (PCA) dimensionality reduction; (3) adopting a bagging-based multi-model voting classification algorithm to enhance robustness. We applied this model to I-band images of a galaxy sample with I_{rm mag}< 25 in the COSMOS field. Compared to the original unsupervised method, the number of clustering groups required by the new method is reduced from 100 to 20. Finally, we managed to classify about 53\% galaxies, significantly improving the classification efficiency. To verify the validity of the morphological classification, we selected massive galaxies with M(*)>10^{10}(M(sun)) for morphological parameter tests. The corresponding rules between the classification results and the physical properties of galaxies on multiple parameter surfaces are consistent with the existing evolution model. Our method has demonstrated the feasibility of using large model encoding to classify galaxy morphology, which not only improves the efficiency of galaxy morphology classification, but also saves time and manpower. Furthermore, in comparison to the original UML model, the enhanced classification performance is more evident in qualitative analysis and has successfully surpassed a greater number of parameter tests.

We present Galaxy Zoo DECaLS: detailed visual morphological classifications for Dark Energy Camera Legacy Survey images of galaxies within the SDSS DR8 footprint. Deeper DECaLS images (r=23.6 vs. r=22.2 from SDSS) reveal spiral arms, weak bars, and tidal features not previously visible in SDSS imaging. To best exploit the greater depth of DECaLS images, volunteers select from a new set of answers designed to improve our sensitivity to mergers and bars. Galaxy Zoo volunteers provide 7.5 million individual classifications over 314,000 galaxies. 140,000 galaxies receive at least 30 classifications, sufficient to accurately measure detailed morphology like bars, and the remainder receive approximately 5. All classifications are used to train an ensemble of Bayesian convolutional neural networks (a state-of-the-art deep learning method) to predict posteriors for the detailed morphology of all 314,000 galaxies. When measured against confident volunteer classifications, the networks are approximately 99% accurate on every question. Morphology is a fundamental feature of every galaxy; our human and machine classifications are an accurate and detailed resource for understanding how galaxies evolve.

We present results on the morphological and structural evolution of a total of 4265 galaxies observed with JWST at 1.5 < z < 8 in the JWST CEERS observations that overlap with the CANDELS EGS field. This is the biggest visually classified sample observed with JWST yet, sim20 times larger than previous studies, and allows us to examine in detail how galaxy structure has changed over this critical epoch. All sources were classified by six individual classifiers using a simple classification scheme aimed to produce disk/spheroid/peculiar classifications, whereby we determine how the relative number of these morphologies evolves since the Universe's first billion years. Additionally, we explore structural and quantitative morphology measurements using Morfometryka, and show that galaxies at z > 3 are not dominated by irregular and peculiar structures, either visually or quantitatively, as previously thought. We find a strong dominance of morphologically selected disk galaxies up to z = 8, a far higher redshift than previously thought possible. We also find that the stellar mass and star formation rate densities are dominated by disk galaxies up to z sim 6, demonstrating that most stars in the universe were likely formed in a disk galaxy. We compare our results to theory to show that the fraction of types we find is predicted by cosmological simulations, and that the Hubble Sequence was already in place as early as one billion years after the Big Bang. Additionally, we make our visual classifications public for the community.

Rheumatoid arthritis (RA) assessment from hand radiographs requires multi-level analysis and modeling of anatomical structures and fine-grained local pathological changes. However, existing public resources do not support such unified multi-level analysis, often lacking full-hand coverage, fine-grained annotations, and consistent integration with clinical scoring systems. In particular, annotations that enable quantitative analysis of bone erosion (BE) remain scarce. RAM-H1200 contains 1,200 hand radiographs collected from six medical centers, with multi-level annotations including (i) whole-hand bone structure instance segmentation, (ii) pixel-level BE masks, (iii) SvdH-defined joint regions of interest, and (iv) joint-level SvdH scores for both BE and joint space narrowing (JSN). It is designed to evaluate whether models can jointly capture anatomical structure, localized erosive pathology, and clinically standardized RA severity from hand radiographs. The proposed BE masks enable, for the first time, quantitative BE analysis beyond coarse categorical grading by providing explicit spatial supervision for lesion extent and morphology. To our knowledge, RAM-H1200 is the first public large-scale benchmark that jointly supports whole-hand bone structure instance segmentation, pixel-level BE delineation, and clinically grounded joint-level SvdH scoring for both BE and JSN. Results across benchmark tasks show that anatomical modeling is substantially more mature than quantitative BE analysis: whole-hand bone segmentation achieves strong performance, whereas BE segmentation remains a major open challenge. By unifying anatomical structure modeling, quantitative lesion analysis, and clinically grounded SvdH scoring, RAM-H1200 provides a single benchmark for comprehensive RA analysis on hand radiographs.

Numerous deep learning-based solutions have been proposed for histopathological image analysis over the past years. While they usually demonstrate exceptionally high accuracy, one key question is whether their precision might be affected by low-level image properties not related to histopathology but caused by microscopy image handling and pre-processing. In this paper, we analyze a popular NCT-CRC-HE-100K colorectal cancer dataset used in numerous prior works and show that both this dataset and the obtained results may be affected by data-specific biases. The most prominent revealed dataset issues are inappropriate color normalization, severe JPEG artifacts inconsistent between different classes, and completely corrupted tissue samples resulting from incorrect image dynamic range handling. We show that even the simplest model using only 3 features per image (red, green and blue color intensities) can demonstrate over 50% accuracy on this 9-class dataset, while using color histogram not explicitly capturing cell morphology features yields over 82% accuracy. Moreover, we show that a basic EfficientNet-B0 ImageNet pretrained model can achieve over 97.7% accuracy on this dataset, outperforming all previously proposed solutions developed for this task, including dedicated foundation histopathological models and large cell morphology-aware neural networks. The NCT-CRC-HE dataset is publicly available and can be freely used to replicate the presented results. The codes and pre-trained models used in this paper are available at https://github.com/gmalivenko/NCT-CRC-HE-experiments

In the applications of proxy-SU(3) model in the context of determining (beta,gamma) values for nuclei across the periodic table, for understanding the preponderance of triaxial shapes in nuclei with Z ge 30, it is seen that one needs not only the highest weight (hw) or leading SU(3) irreducible representation (irrep) (lambda_H, mu_H) but also the lower SU(3) irreps (lambda ,mu) such that 2lambda + mu =2lambda_H + mu_H-3r with r=0,1 and 2 [Bonatsos et al., Symmetry {\bf 16}, 1625 (2024)]. These give the next highest weight (nhw) irrep, next-to-next highest irrep (nnhw) and so on. Recently, it is shown that for nuclei with 32 le Z,N le 46, there will be not only proxy-SU(3) but also proxy-SU(4) symmetry [Kota and Sahu, Physica Scripta {\bf 99}, 065306 (2024)]. Following these developments, presented in this paper are the SU(3) irreps (lambda ,mu) with 2lambda + mu =2lambda_H + mu_H-3r, r=0,1,2 for various isotopes of Ge, Se, Kr, Sr, Zr, Mo, Ru and Pd (with 32 le N le 46) assuming good proxy-SU(4) symmetry. A simple method for obtaining the SU(3) irreps is described and applied. The tabulations for proxy-SU(3) irreps provided in this paper will be useful in further investigations of triaxial shapes in these nuclei.

Cell instance segmentation (CIS) is crucial for identifying individual cell morphologies in histopathological images, providing valuable insights for biological and medical research. While unsupervised CIS (UCIS) models aim to reduce the heavy reliance on labor-intensive image annotations, they fail to accurately capture cell boundaries, causing missed detections and poor performance. Recognizing the absence of error-free instances as a key limitation, we present COIN (COnfidence score-guided INstance distillation), a novel annotation-free framework with three key steps: (1) Increasing the sensitivity for the presence of error-free instances via unsupervised semantic segmentation with optimal transport, leveraging its ability to discriminate spatially minor instances, (2) Instance-level confidence scoring to measure the consistency between model prediction and refined mask and identify highly confident instances, offering an alternative to ground truth annotations, and (3) Progressive expansion of confidence with recursive self-distillation. Extensive experiments across six datasets show COIN outperforming existing UCIS methods, even surpassing semi- and weakly-supervised approaches across all metrics on the MoNuSeg and TNBC datasets. The code is available at https://github.com/shjo-april/COIN.

Single-nucleus RNA sequencing (snRNA-seq) has significantly advanced our understanding of the disease etiology of neurodegenerative disorders. However, the low quality of specimens derived from postmortem brain tissues, combined with the high variability caused by disease heterogeneity, makes it challenging to integrate snRNA-seq data from multiple sources for precise analyses. To address these challenges, we present scMamba, a pre-trained model designed to improve the quality and utility of snRNA-seq analysis, with a particular focus on neurodegenerative diseases. Inspired by the recent Mamba model, scMamba introduces a novel architecture that incorporates a linear adapter layer, gene embeddings, and bidirectional Mamba blocks, enabling efficient processing of snRNA-seq data while preserving information from the raw input. Notably, scMamba learns generalizable features of cells and genes through pre-training on snRNA-seq data, without relying on dimension reduction or selection of highly variable genes. We demonstrate that scMamba outperforms benchmark methods in various downstream tasks, including cell type annotation, doublet detection, imputation, and the identification of differentially expressed genes.

The majority of galaxies in the local Universe exhibit spiral structure with a variety of forms. Many galaxies possess two prominent spiral arms, some have more, while others display a many-armed flocculent appearance. Spiral arms are associated with enhanced gas content and star-formation in the disks of low-redshift galaxies, so are important in the understanding of star-formation in the local universe. As both the visual appearance of spiral structure, and the mechanisms responsible for it vary from galaxy to galaxy, a reliable method for defining spiral samples with different visual morphologies is required. In this paper, we develop a new debiasing method to reliably correct for redshift-dependent bias in Galaxy Zoo 2, and release the new set of debiased classifications. Using these, a luminosity-limited sample of ~18,000 Sloan Digital Sky Survey spiral galaxies is defined, which are then further sub-categorised by spiral arm number. In order to explore how different spiral galaxies form, the demographics of spiral galaxies with different spiral arm numbers are compared. It is found that whilst all spiral galaxies occupy similar ranges of stellar mass and environment, many-armed galaxies display much bluer colours than their two-armed counterparts. We conclude that two-armed structure is ubiquitous in star-forming disks, whereas many-armed spiral structure appears to be a short-lived phase, associated with more recent, stochastic star-formation activity.

Spatial transcriptomics (ST) provides unprecedented insights into tumor heterogeneity by capturing spatially resolved gene expression, yet its high experimental cost hinders large-scale adoption. Consequently, computational approaches that predict spatial gene expression directly from hematoxylin and eosin slides, termed virtual ST, have rapidly emerged. Despite this progress, assessing advances in the field remains difficult due to insufficient benchmarking: prior studies rely on small, heterogeneous datasets, inconsistent training and inference pipelines, and limited evaluation of biological interpretability and model robustness. To address these gaps, we present STP-BENCH, a standardized benchmark for virtual ST models. STP-BENCH comprises six cancer types spanning two ST platforms (Visium and Xenium), with each training dataset containing more than 30,000 spots and at least 15 slides to ensure statistical reliability. We evaluate 21 predictive approaches, re-implemented with a unified pathology foundation model as the morphological encoder when architecturally applicable. Beyond conventional benchmarks that report average predictive accuracy on highly variable genes, we systematically examine which genes and gene sets are recoverable from histomorphology. We further evaluate the downstream biological utility of predicted profiles through cell-type deconvolution and spatial domain identification, and assess model reliability under domain shifts and data scaling. Notably, unified morphological encoding substantially re-orders model rankings established in prior studies, indicating that architectural innovations and image encoding have been conflated in previous evaluations. We publicly release STP-BENCH to support reproducibility and serve as a community benchmark at https://github.com/NEXGEM/STP-Bench.

Instance segmentation of neurons in volumetric light microscopy images of nervous systems enables groundbreaking research in neuroscience by facilitating joint functional and morphological analyses of neural circuits at cellular resolution. Yet said multi-neuron light microscopy data exhibits extremely challenging properties for the task of instance segmentation: Individual neurons have long-ranging, thin filamentous and widely branching morphologies, multiple neurons are tightly inter-weaved, and partial volume effects, uneven illumination and noise inherent to light microscopy severely impede local disentangling as well as long-range tracing of individual neurons. These properties reflect a current key challenge in machine learning research, namely to effectively capture long-range dependencies in the data. While respective methodological research is buzzing, to date methods are typically benchmarked on synthetic datasets. To address this gap, we release the FlyLight Instance Segmentation Benchmark (FISBe) dataset, the first publicly available multi-neuron light microscopy dataset with pixel-wise annotations. In addition, we define a set of instance segmentation metrics for benchmarking that we designed to be meaningful with regard to downstream analyses. Lastly, we provide three baselines to kick off a competition that we envision to both advance the field of machine learning regarding methodology for capturing long-range data dependencies, and facilitate scientific discovery in basic neuroscience.

Recent advancements in image-based profiling techniques have enabled the collection of high-volume cell morphology data, allowing new molecular embedding models to learn from the experimental phenotypic perturbations of a molecule in a cell. Previously, we developed Molecule-Morphology Contrastive Pretraining (MoCoP), a strategy for aligning small molecule embeddings to morphology fingerprints extracted through CellProfiler. The resulting molecular representation showed transferable performance for quantitative structure--activity relationship (QSAR) prediction tasks. Here, we extend the method by using a deep-learning-based cell image encoding pipeline to extract more feature-rich morphology profiles and align them to the molecular embeddings through contrastive learning. The new embeddings encode more accurate information on how molecules perturb cell morphology and enable improvements for QSAR predictions through either fixed-embedding linear probes or fully flexible fine-tuning. Morphology retrieval performance scales log-linearly with training data size, suggesting continued improvements as larger datasets become available. The improved MoCoP v2 also achieves superior performance on toxicity prediction and competitive results on ADME and activity benchmarks, when compared with existing molecular embedding models that use both cell morphology and transcriptomic data during training.

Spatial transcriptomics (ST) enables interrogating the molecular composition of tissue with ever-increasing resolution, depth, and sensitivity. However, costs, rapidly evolving technology, and lack of standards have constrained computational methods in ST to narrow tasks and small cohorts. In addition, the underlying tissue morphology as reflected by H&E-stained whole slide images (WSIs) encodes rich information often overlooked in ST studies. Here, we introduce HEST-1k, a collection of 1,108 spatial transcriptomic profiles, each linked to a WSI and metadata. HEST-1k was assembled using HEST-Library from 131 public and internal cohorts encompassing 25 organs, two species (Homo Sapiens and Mus Musculus), and 320 cancer samples from 25 cancer types. HEST-1k processing enabled the identification of 1.5 million expression--morphology pairs and 60 million nuclei. HEST-1k is tested on three use cases: (1) benchmarking foundation models for histopathology (HEST-Benchmark), (2) biomarker identification, and (3) multimodal representation learning. HEST-1k, HEST-Library, and HEST-Benchmark can be freely accessed via https://github.com/mahmoodlab/hest.

The morphological attributes of retinal vessels, such as length, width, tortuosity and branching pattern and angles, play an important role in diagnosis, screening, treatment, and evaluation of various cardiovascular and ophthalmologic diseases such as diabetes, hypertension and arteriosclerosis. The crucial step before extracting these morphological characteristics of retinal vessels from retinal fundus images is vessel segmentation. In this work, we propose a method for retinal vessel segmentation based on fully convolutional networks. Thousands of patches are extracted from each retinal image and then fed into the network, and data argumentation is applied by rotating extracted patches. Two architectures of fully convolutional networks, U-Net and LadderNet, are used for vessel segmentation. The performance of our method is evaluated on three public datasets: DRIVE, STARE, and CHASE\_DB1. Experimental results of our method show superior performance compared to recent state-of-the-art methods.

Content generation modeling has emerged as a promising direction in computational pathology, offering capabilities such as data-efficient learning, synthetic data augmentation, and task-oriented generation across diverse diagnostic tasks. This review provides a comprehensive synthesis of recent progress in the field, organized into four key domains: image generation, text generation, molecular profile-morphology generation, and other specialized generation applications. By analyzing over 150 representative studies, we trace the evolution of content generation architectures -- from early generative adversarial networks to recent advances in diffusion models and generative vision-language models. We further examine the datasets and evaluation protocols commonly used in this domain and highlight ongoing limitations, including challenges in generating high-fidelity whole slide images, clinical interpretability, and concerns related to the ethical and legal implications of synthetic data. The review concludes with a discussion of open challenges and prospective research directions, with an emphasis on developing integrated and clinically deployable generation systems. This work aims to provide a foundational reference for researchers and practitioners developing content generation models in computational pathology.

Synthetic data generation in histopathology faces unique challenges: preserving tissue heterogeneity, capturing subtle morphological features, and scaling to unannotated datasets. We present a latent diffusion model that generates realistic heterogeneous histopathology images through a novel dual-conditioning approach combining semantic segmentation maps with tissue-specific visual crops. Unlike existing methods that rely on text prompts or abstract visual embeddings, our approach preserves critical morphological details by directly incorporating raw tissue crops from corresponding semantic regions. For annotated datasets (i.e., Camelyon16, Panda), we extract patches ensuring 20-80% tissue heterogeneity. For unannotated data (i.e., TCGA), we introduce a self-supervised extension that clusters whole-slide images into 100 tissue types using foundation model embeddings, automatically generating pseudo-semantic maps for training. Our method synthesizes high-fidelity images with precise region-wise annotations, achieving superior performance on downstream segmentation tasks. When evaluated on annotated datasets, models trained on our synthetic data show competitive performance to those trained on real data, demonstrating the utility of controlled heterogeneous tissue generation. In quantitative evaluation, prompt-guided synthesis reduces Frechet Distance by up to 6X on Camelyon16 (from 430.1 to 72.0) and yields 2-3x lower FD across Panda and TCGA. Downstream DeepLabv3+ models trained solely on synthetic data attain test IoU of 0.71 and 0.95 on Camelyon16 and Panda, within 1-2% of real-data baselines (0.72 and 0.96). By scaling to 11,765 TCGA whole-slide images without manual annotations, our framework offers a practical solution for an urgent need for generating diverse, annotated histopathology data, addressing a critical bottleneck in computational pathology.

Induced pluripotent stem cell (iPSC) culture increasingly relies on segmentation foundation models, yet deployment on laboratory CPUs and edge hardware requires compression schemes that are both efficient and auditable. We present a deployment-oriented evaluation of compressed Cellpose-SAM using a pre-specified retention criterion: the 95% cluster-bootstrap interval of mean change from FP32 must remain above a fixed -0.02 margin for every imaging modality. On a stratified 176-field panel spanning BBBC038 nuclei, BBBC039 U2OS fluorescence, and NIST iPSC images across density regimes, weight-only W8A16 preserves instance F1 across all modalities. A sensitivity-guided mixed W4/W8 scheme, using four INT8 exceptions, achieves a 6.76x reduction in weight storage with no observed catastrophic failures (0/176 fields), matching W8A16 at this sample size. In contrast, ternary weight-only quantization achieves 12.08x compression but fails catastrophically on 169/176 fields. These results demonstrate that compression should be evaluated by modality-stratified downstream retention rather than single-number accuracy, and establish a reproducible protocol for auditing compressed foundation models in regulated stem-cell imaging.

Cytology is essential for cancer diagnostics and screening due to its minimally invasive nature. However, the development of robust deep learning models for digital cytology is challenging due to the heterogeneity in staining and preparation methods of samples, differences across organs, and the limited availability of large, diverse, annotated datasets. Developing a task-specific model for every cytology application is impractical and non-cytology-specific foundation models struggle to generalize to tasks in this domain where the emphasis is on cell morphology. To address these challenges, we introduce CytoFM, the first cytology self-supervised foundation model. Using iBOT, a self-supervised Vision Transformer (ViT) training framework incorporating masked image modeling and self-distillation, we pretrain CytoFM on a diverse collection of cytology datasets to learn robust, transferable representations. We evaluate CytoFM on multiple downstream cytology tasks, including breast cancer classification and cell type identification, using an attention-based multiple instance learning framework. Our results demonstrate that CytoFM performs better on two out of three downstream tasks than existing foundation models pretrained on histopathology (UNI) or natural images (iBOT-Imagenet). Visualizations of learned representations demonstrate our model is able to attend to cytologically relevant features. Despite a small pre-training dataset, CytoFM's promising results highlight the ability of task-agnostic pre-training approaches to learn robust and generalizable features from cytology data.

The evolution of biological morphology is critical for understanding the diversity of the natural world, yet traditional analyses often involve subjective biases in the selection and coding of morphological traits. This study employs deep learning techniques, utilising a ResNet34 model capable of recognising over 10,000 bird species, to explore avian morphological evolution. We extract weights from the model's final fully connected (fc) layer and investigate the semantic alignment between the high-dimensional embedding space learned by the model and biological phenotypes. The results demonstrate that the high-dimensional embedding space encodes phenotypic convergence. Subsequently, we assess the morphological disparity among various taxa and evaluate the association between morphological disparity and species richness, demonstrating that species richness is the primary driver of morphospace expansion. Moreover, the disparity-through-time analysis reveals a visual "early burst" after the K-Pg extinction. While mainly aimed at evolutionary analysis, this study also provides insights into the interpretability of Deep Neural Networks. We demonstrate that hierarchical semantic structures (biological taxonomy) emerged in the high-dimensional embedding space despite being trained on flat labels. Furthermore, through adversarial examples, we provide evidence that our model in this task can overcome texture bias and learn holistic shape representations (body plans), challenging the prevailing view that CNNs rely primarily on local textures.

We present the results of high-resolution (sim1~au) Atacama Large Millimeter/submillimeter Array (ALMA) observations of the TW~Hya protoplanetary disk in the Band 6 dust continuum, as well as the ^13CO and C^18O J=2--1 emission lines. The primary focus of this study is to investigate the kinematics, internal morphology, and local gas environment of the prominent dust blob at a radius of 52~au. By comparing our 2021 data with archival observations from 2017, we detect the proper motion of the blob. The measured azimuthal velocity of 3.3pm0.9~km~s^{-1} is fully consistent with local Keplerian rotation. Combined with the lack of significant radial migration over the four-year baseline, this confirms that the structure is robustly co-moving with the disk system. Crucially, our high-resolution continuum map resolves the blob into a distinct double-peaked morphology separated by sim1.7~au azimuthally. We robustly validate this double-peaked substructure by reproducing it in the independent 2017 dataset using a sparse-modeling image reconstruction technique. We discuss potential physical origins for this double-peaked morphology, including an inclined circumplanetary disk with an inner dust cavity, the roots of planet-induced spiral arms, or alternative hydrodynamic scenarios that do not involve an actively accreting planet such as the U-turn trajectory of secondary dust or a short-lived hydrodynamic gas vortex. We detect no compact gas emission counterparts associated with the continuum blob. Since these CO lines likely trace optically thick upper atmospheric layers, the absence of localized vertical gas perturbations suggests that if an embedded planet is responsible for the dust structure, its mass must be exceptionally low.

Polyps in the colon are widely known cancer precursors identified by colonoscopy. Whilst most polyps are benign, the polyp's number, size and surface structure are linked to the risk of colon cancer. Several methods have been developed to automate polyp detection and segmentation. However, the main issue is that they are not tested rigorously on a large multicentre purpose-built dataset, one reason being the lack of a comprehensive public dataset. As a result, the developed methods may not generalise to different population datasets. To this extent, we have curated a dataset from six unique centres incorporating more than 300 patients. The dataset includes both single frame and sequence data with 3762 annotated polyp labels with precise delineation of polyp boundaries verified by six senior gastroenterologists. To our knowledge, this is the most comprehensive detection and pixel-level segmentation dataset (referred to as PolypGen) curated by a team of computational scientists and expert gastroenterologists. The paper provides insight into data construction and annotation strategies, quality assurance, and technical validation. Our dataset can be downloaded from https://doi.org/10.7303/syn26376615.

Neuronal morphology encodes critical information about circuit function, development, and disease, yet current methods analyze topology or graph structure in isolation. We introduce GraPHFormer, a multimodal architecture that unifies these complementary views through CLIP-style contrastive learning. Our vision branch processes a novel three-channel persistence image encoding unweighted, persistence-weighted, and radius-weighted topological densities via DINOv2-ViT-S. In parallel, a TreeLSTM encoder captures geometric and radial attributes from skeleton graphs. Both project to a shared embedding space trained with symmetric InfoNCE loss, augmented by persistence-space transformations that preserve topological semantics. Evaluated on six benchmarks (BIL-6, ACT-4, JML-4, N7, M1-Cell, M1-REG) spanning self-supervised and supervised settings, GraPHFormer achieves state-of-the-art performance on five benchmarks, significantly outperforming topology-only, graph-only, and morphometrics baselines. We demonstrate practical utility by discriminating glial morphologies across cortical regions and species, and detecting signatures of developmental and degenerative processes. Code: https://github.com/Uzshah/GraPHFormer

Colon Cancer is one of the most common types of cancer. The treatment is planned to depend on the grade or stage of cancer. One of the preconditions for grading of colon cancer is to segment the glandular structures of tissues. Manual segmentation method is very time-consuming, and it leads to life risk for the patients. The principal objective of this project is to assist the pathologist to accurate detection of colon cancer. In this paper, the authors have proposed an algorithm for an automatic segmentation of glands in colon histology using local intensity and texture features. Here the dataset images are cropped into patches with different window sizes and taken the intensity of those patches, and also calculated texture-based features. Random forest classifier has been used to classify this patch into different labels. A multilevel random forest technique in a hierarchical way is proposed. This solution is fast, accurate and it is very much applicable in a clinical setup.

One of the major difficulties in medical image segmentation is the high variability of these images, which is caused by their origin (multi-centre), the acquisition protocols (multi-parametric), as well as the variability of human anatomy, the severity of the illness, the effect of age and gender, among others. The problem addressed in this work is the automatic semantic segmentation of lumbar spine Magnetic Resonance images using convolutional neural networks. The purpose is to assign a class label to each pixel of an image. Classes were defined by radiologists and correspond to different structural elements like vertebrae, intervertebral discs, nerves, blood vessels, and other tissues. The proposed network topologies are variants of the U-Net architecture. Several complementary blocks were used to define the variants: Three types of convolutional blocks, spatial attention models, deep supervision and multilevel feature extractor. This document describes the topologies and analyses the results of the neural network designs that obtained the most accurate segmentations. Several of the proposed designs outperform the standard U-Net used as baseline, especially when used in ensembles where the output of multiple neural networks is combined according to different strategies.

The correlation between black hole mass, M_{rm bh}, and stellar velocity dispersion, σ_0, is revisited using 137 galaxies with quantitative bar strengths and enhanced morphological awareness. Interpreted within the `Triangal' evolutionary framework, gas-rich and gas-poor assembly pathways emerge in the M_{rm bh}-σ_0 diagram. To quantify these scaling relations, a symmetric Bayesian hierarchical regression code, dubbed the Symmetric COvariance Population Estimator (SCOPE), is introduced. Unlike conditional estimators (e.g., LINMIX), SCOPE derives the intrinsic population covariance, natively accommodating asymmetric measurement errors while guaranteeing directional invariance between axes. Primeval, dust-poor S0 galaxies (including dwarf early-type galaxies with R_{rm e,gal} ~ 1 kpc) follow a shallow relation (M_{rm bh}proptoσ_0^{2.5--3.1}). Explained via the virial theorem, this flattening reframes expectations for intermediate-mass black holes. In contrast, tracing the `Disc Down-sizing' sequence - where dry mergers erase discs - yields a steep relation for massive elliptical and ellicular galaxies (M_{rm bh}proptoσ_0^{7.8pm1.4}). Applying a single, monolithic scaling relation across all morphologies inadvertently averages over different formation histories, potentially skewing AGN virial f-factor calibrations and systematically under-predicting the ultra-massive black holes needed to generate the nanohertz gravitational wave background. Furthermore, strongly barred, dust-poor S0 galaxies appear offset to higher σ_0, while this dynamical signature is lost in the complexities of spiral galaxies. Ultimately, these morphology-dependent relations provide physically-motivated benchmarks for cosmological simulations and a framework for disentangling regimes driven by AGN feedback from those driven by mergers.

Instance segmentation of overlapping cells in microscopy remains challenging due to semi-transparent structures that produce weak boundaries and mixed visual evidence in overlap regions. Existing methods address this through local regions of interest or shape priors but lack global reasoning across overlapping objects. We present QCell, a novel query-based model that de-overlaps cell instances in microscopy scenes. Our approach combines (i) an instance recombination module that decomposes and recombines query representations in latent space, enabling the model to reason about complete object structure under overlap, and (ii) a contrastive query alignment objective that combines distinctive instance feature learning and separation of overlapping cell queries. We additionally introduce a new Organoid dataset benchmark for overlapping cell segmentation. We show that QCell outperforms state-of-the-art methods across multiple benchmarks, achieving +2.2 AP and +2.7 AJI on ISBI2014. Code is available at https://github.com/SlavkoPrytula/QCell

Morphological neural networks, or layers, can be a powerful tool to boost the progress in mathematical morphology, either on theoretical aspects such as the representation of complete lattice operators, or in the development of image processing pipelines. However, these architectures turn out to be difficult to train when they count more than a few morphological layers, at least within popular machine learning frameworks which use gradient descent based optimization algorithms. In this paper we investigate the potential and limitations of differentiation based approaches and back-propagation applied to morphological networks, in light of the non-smooth optimization concept of Bouligand derivative. We provide insights and first theoretical guidelines, in particular regarding initialization and learning rates.

Mitotic figure (MF) detection in histopathology images is challenging due to large variations in slide scanners, staining protocols, tissue types, and the presence of artifacts. This paper presents a collection of training techniques - a bag of tricks - that enable robust, real-time MF detection across diverse domains. We build on the efficient RTMDet single stage object detector to achieve high inference speed suitable for clinical deployment. Our method addresses scanner variability and tumor heterogeneity via extensive multi-domain training data, balanced sampling, and careful augmentation. Additionally, we employ targeted, hard negative mining on necrotic and debris tissue to reduce false positives. In a grouped 5-fold cross-validation across multiple MF datasets, our model achieves an F1 score between 0.78 and 0.84. On the preliminary test set of the MItosis DOmain Generalization (MIDOG) 2025 challenge, our single-stage RTMDet-S based approach reaches an F1 of 0.81, outperforming larger models and demonstrating adaptability to new, unfamiliar domains. The proposed solution offers a practical trade-off between accuracy and speed, making it attractive for real-world clinical adoption.

Modern optical microscopes are fully motorised; however, transforming them into truly smart systems requires real-time adjustment of acquisition settings in response to detected objects and dynamic biological events. At the core are classification algorithms that commonly depend on customised softwares and are generally designed for narrowly-defined biological applications. In addition, they often require substantial annotated datasets for effective training. We introduce a semi-supervised generative adversarial network (SGAN) for robust cell-cycle stage classification under low-resource conditions, adaptable to diverse cellular structures. The framework combines unlabelled microscopy images with synthetically generated samples to mitigate limited annotation, while preserving stable performance even when the unlabelled subset is class-imbalanced. Tested on the Mitocheck dataset, which features five mitosis classes, the model achieved 93 pm 2% accuracy using only 80 labelled per class and 600 unlabelled images. The proposed algorithm is generic and can be readily adapted to new labeling schemes, classification targets, cell lines, or microscopy modalities through transfer learning. SGAN is well suited for integration into automated microscopes, enabling efficient and adaptable image analysis across diverse biological and microscopy applications.

Whole Slide Images (WSIs) exhibit hierarchical structure, where diagnostic information emerges from cellular morphology, regional tissue organization, and global context. Existing Computational Pathology (CPath) Multimodal Large Language Models (MLLMs) typically compress an entire WSI into a single embedding, which hinders fine-grained grounding and ignores how pathologists synthesize evidence across different scales. We introduce MLLM-HWSI, a Hierarchical WSI-level MLLM that aligns visual features with pathology language at four distinct scales, cell as word, patch as phrase, region as sentence, and WSI as paragraph to support interpretable evidence-grounded reasoning. MLLM-HWSI decomposes each WSI into multi-scale embeddings with scale-specific projectors and jointly enforces (i) a hierarchical contrastive objective and (ii) a cross-scale consistency loss, preserving semantic coherence from cells to the WSI. We compute diagnostically relevant patches and aggregate segmented cell embeddings into a compact cellular token per-patch using a lightweight Cell-Cell Attention Fusion (CCAF) transformer. The projected multi-scale tokens are fused with text tokens and fed to an instruction-tuned LLM for open-ended reasoning, VQA, report, and caption generation tasks. Trained in three stages, MLLM-HWSI achieves new SOTA results on 13 WSI-level benchmarks across six CPath tasks. By aligning language with multi-scale visual evidence, MLLM-HWSI provides accurate, interpretable outputs that mirror diagnostic workflows and advance holistic WSI understanding. Code is available at: https://github.com/BasitAlawode/HWSI-MLLM{GitHub}.

Peripheral Blood Smear (PBS) is a critical microscopic examination in hematopathology that yields whole-slide imaging (WSI). Unlike solid tissue pathology, PBS interpretation focuses on individual cell morphologies rather than tissue architecture, making it distinct in both visual characteristics and diagnostic reasoning. However, current multimodal large language models (MLLMs) for pathology are primarily developed on solid-tissue WSIs and struggle to generalize to PBS. To bridge this gap, we construct PBSInstr, the first vision-language dataset for PBS interpretation, comprising 353 PBS WSIs paired with microscopic impression paragraphs and 29k cell-level image crops annotated with cell type labels and morphological descriptions. To facilitate instruction tuning, PBSInstr further includes 27k question-answer (QA) pairs for cell crops and 1,286 QA pairs for PBS slides. Building upon PBSInstr, we develop PBS-VL, a hematopathology-tailored vision-language model for multi-level PBS interpretation at both cell and slide levels. To comprehensively evaluate PBS understanding, we construct PBSBench, a visual question answering (VQA) benchmark featuring four question categories and six PBS interpretation tasks. Experiments show that PBS-VL outperforms existing general-purpose and pathology MLLMs, underscoring the value of PBS-specific data. We release our code, datasets, and model weights to facilitate future research. Our proposed framework lays the foundation for developing practical AI assistants supporting decision-making in hematopathology.

The tumor immune microenvironment (TIME) in non-small cell lung cancer (NSCLC) histopathology contains morphological and molecular characteristics predictive of immunotherapy response. Computational quantification of TIME characteristics, such as cell detection and tissue segmentation, can support biomarker development. However, currently available digital pathology datasets of NSCLC for the development of cell detection or tissue segmentation algorithms are limited in scope, lack annotations of clinically prevalent metastatic sites, and forgo molecular information such as PD-L1 immunohistochemistry (IHC). To fill this gap, we introduce the IGNITE data toolkit, a multi-stain, multi-centric, and multi-scanner dataset of annotated NSCLC whole-slide images. We publicly release 887 fully annotated regions of interest from 155 unique patients across three complementary tasks: (i) multi-class semantic segmentation of tissue compartments in H&E-stained slides, with 16 classes spanning primary and metastatic NSCLC, (ii) nuclei detection, and (iii) PD-L1 positive tumor cell detection in PD-L1 IHC slides. To the best of our knowledge, this is the first public NSCLC dataset with manual annotations of H&E in metastatic sites and PD-L1 IHC.

Single cell segmentation is critical and challenging in live cell imaging data analysis. Traditional image processing methods and tools require time-consuming and labor-intensive efforts of manually fine-tuning parameters. Slight variations of image setting may lead to poor segmentation results. Recent development of deep convolutional neural networks(CNN) provides a potentially efficient, general and robust method for segmentation. Most existing CNN-based methods treat segmentation as a pixel-wise classification problem. However, three unique problems of cell images adversely affect segmentation accuracy: lack of established training dataset, few pixels on cell boundaries, and ubiquitous blurry features. The problem becomes especially severe with densely packed cells, where a pixel-wise classification method tends to identify two neighboring cells with blurry shared boundary as one cell, leading to poor cell count accuracy and affecting subsequent analysis. Here we developed a different learning strategy that combines strengths of CNN and watershed algorithm. The method first trains a CNN to learn Euclidean distance transform of binary masks corresponding to the input images. Then another CNN is trained to detect individual cells in the Euclidean distance transform. In the third step, the watershed algorithm takes the outputs from the previous steps as inputs and performs the segmentation. We tested the combined method and various forms of the pixel-wise classification algorithm on segmenting fluorescence and transmitted light images. The new method achieves similar pixel accuracy but significant higher cell count accuracy than pixel-wise classification methods do, and the advantage is most obvious when applying on noisy images of densely packed cells.

Over the past decade, the revolution in single-cell sequencing has enabled the simultaneous molecular profiling of various modalities across thousands of individual cells, allowing scientists to investigate the diverse functions of complex tissues and uncover underlying disease mechanisms. Among all the analytical steps, assigning individual cells to specific types is fundamental for understanding cellular heterogeneity. However, this process is usually labor-intensive and requires extensive expert knowledge. Recent advances in large language models (LLMs) have demonstrated their ability to efficiently process and synthesize vast corpora of text to automatically extract essential biological knowledge, such as marker genes, potentially promoting more efficient and automated cell type annotations. To thoroughly evaluate the capability of modern instruction-tuned LLMs in automating the cell type identification process, we introduce SOAR, a comprehensive benchmarking study of LLMs for cell type annotation tasks in single-cell genomics. Specifically, we assess the performance of 8 instruction-tuned LLMs across 11 datasets, spanning multiple cell types and species. Our study explores the potential of LLMs to accurately classify and annotate cell types in single-cell RNA sequencing (scRNA-seq) data, while extending their application to multiomics data through cross-modality translation. Additionally, we evaluate the effectiveness of chain-of-thought (CoT) prompting techniques in generating detailed biological insights during the annotation process. The results demonstrate that LLMs can provide robust interpretations of single-cell data without requiring additional fine-tuning, advancing the automation of cell type annotation in genomics research.