Automated and Scalable SEM Image Analysis of Perovskite Solar Cell Materials via a Deep Segmentation Framework

Scanning Electron Microscopy (SEM) is indispensable for characterizing the microstructure of thin films during perovskite solar cell fabrication. Accurate identification and quantification of lead iodide and perovskite phases are critical because residual lead iodide strongly influences crystallization pathways and defect formation, while the morphology of perovskite grains governs carrier transport and device stability. Yet current SEM image analysis is still largely manual, limiting throughput and consistency. Here, we present an automated deep learning-based framework for SEM image segmentation that enables precise and efficient identification of lead iodide, perovskite and defect domains across diverse morphologies. Built upon an improved YOLOv8x architecture, our model named PerovSegNet incorporates two novel modules: (i) Adaptive Shuffle Dilated Convolution Block, which enhances multi-scale and fine-grained feature extraction through group convolutions and channel mixing; and (ii) Separable Adaptive Downsampling module, which jointly preserves fine-scale textures and large-scale structures for more robust boundary recognition. Trained on an augmented dataset of 10,994 SEM images, PerovSegNet achieves a mean Average Precision of 87.25% with 265.4 Giga Floating Point Operations, outperforming the baseline YOLOv8x-seg by 4.08%, while reducing model size and computational load by 24.43% and 25.22%, respectively. Beyond segmentation, the framework provides quantitative grain-level metrics, such as lead iodide/perovskite area and count, which can serve as reliable indicators of crystallization efficiency and microstructural quality. These capabilities establish PerovSegNet as a scalable tool for real-time process monitoring and data-driven optimization of perovskite thin-film fabrication.The source code is available at:https://github.com/wlyyj/PerovSegNet/tree/master.

A Multicentric Dataset for Training and Benchmarking Breast Cancer Segmentation in H&E Slides

Automated semantic segmentation of whole-slide images (WSIs) stained with hematoxylin and eosin (H&E) is essential for large-scale artificial intelligence-based biomarker analysis in breast cancer. However, existing public datasets for breast cancer segmentation lack the morphological diversity needed to support model generalizability and robust biomarker validation across heterogeneous patient cohorts. We introduce BrEast cancEr hisTopathoLogy sEgmentation (BEETLE), a dataset for multiclass semantic segmentation of H&E-stained breast cancer WSIs. It consists of 587 biopsies and resections from three collaborating clinical centers and two public datasets, digitized using seven scanners, and covers all molecular subtypes and histological grades. Using diverse annotation strategies, we collected annotations across four classes - invasive epithelium, non-invasive epithelium, necrosis, and other - with particular focus on morphologies underrepresented in existing datasets, such as ductal carcinoma in situ and dispersed lobular tumor cells. The dataset's diversity and relevance to the rapidly growing field of automated biomarker quantification in breast cancer ensure its high potential for reuse. Finally, we provide a well-curated, multicentric external evaluation set to enable standardized benchmarking of breast cancer segmentation models.

OCELOT 2023: Cell Detection from Cell-Tissue Interaction Challenge

Pathologists routinely alternate between different magnifications when examining Whole-Slide Images, allowing them to evaluate both broad tissue morphology and intricate cellular details to form comprehensive diagnoses. However, existing deep learning-based cell detection models struggle to replicate these behaviors and learn the interdependent semantics between structures at different magnifications. A key barrier in the field is the lack of datasets with multi-scale overlapping cell and tissue annotations. The OCELOT 2023 challenge was initiated to gather insights from the community to validate the hypothesis that understanding cell and tissue (cell-tissue) interactions is crucial for achieving human-level performance, and to accelerate the research in this field. The challenge dataset includes overlapping cell detection and tissue segmentation annotations from six organs, comprising 673 pairs sourced from 306 The Cancer Genome Atlas (TCGA) Whole-Slide Images with hematoxylin and eosin staining, divided into training, validation, and test subsets. Participants presented models that significantly enhanced the understanding of cell-tissue relationships. Top entries achieved up to a 7.99 increase in F1-score on the test set compared to the baseline cell-only model that did not incorporate cell-tissue relationships. This is a substantial improvement in performance over traditional cell-only detection methods, demonstrating the need for incorporating multi-scale semantics into the models. This paper provides a comparative analysis of the methods used by participants, highlighting innovative strategies implemented in the OCELOT 2023 challenge.

Sketchpose: Learning to Segment Cells with Partial Annotations

The most popular networks used for cell segmentation (e.g. Cellpose, Stardist, HoverNet,...) rely on a prediction of a distance map. It yields unprecedented accuracy but hinges on fully annotated datasets. This is a serious limitation to generate training sets and perform transfer learning. In this paper, we propose a method that still relies on the distance map and handles partially annotated objects. We evaluate the performance of the proposed approach in the contexts of frugal learning, transfer learning and regular learning on regular databases. Our experiments show that it can lead to substantial savings in time and resources without sacrificing segmentation quality. The proposed algorithm is embedded in a user-friendly Napari plugin.

UNIV: Unified Foundation Model for Infrared and Visible Modalities

The demand for joint RGB-visible and infrared perception is growing rapidly, particularly to achieve robust performance under diverse weather conditions. Although pre-trained models for RGB-visible and infrared data excel in their respective domains, they often underperform in multimodal scenarios, such as autonomous vehicles equipped with both sensors. To address this challenge, we propose a biologically inspired UNified foundation model for Infrared and Visible modalities (UNIV), featuring two key innovations. First, we introduce Patch-wise Cross-modality Contrastive Learning (PCCL), an attention-guided distillation framework that mimics retinal horizontal cells' lateral inhibition, which enables effective cross-modal feature alignment while remaining compatible with any transformer-based architecture. Second, our dual-knowledge preservation mechanism emulates the retina's bipolar cell signal routing - combining LoRA adapters (2% added parameters) with synchronous distillation to prevent catastrophic forgetting, thereby replicating the retina's photopic (cone-driven) and scotopic (rod-driven) functionality. To support cross-modal learning, we introduce the MVIP dataset, the most comprehensive visible-infrared benchmark to date. It contains 98,992 precisely aligned image pairs spanning diverse scenarios. Extensive experiments demonstrate UNIV's superior performance on infrared tasks (+1.7 mIoU in semantic segmentation and +0.7 mAP in object detection) while maintaining 99%+ of the baseline performance on visible RGB tasks. Our code is available at https://github.com/fangyuanmao/UNIV.

Maybe you don't need a U-Net: convolutional feature upsampling for materials micrograph segmentation

Feature foundation models - usually vision transformers - offer rich semantic descriptors of images, useful for downstream tasks such as (interactive) segmentation and object detection. For computational efficiency these descriptors are often patch-based, and so struggle to represent the fine features often present in micrographs; they also struggle with the large image sizes present in materials and biological image analysis. In this work, we train a convolutional neural network to upsample low-resolution (i.e, large patch size) foundation model features with reference to the input image. We apply this upsampler network (without any further training) to efficiently featurise and then segment a variety of microscopy images, including plant cells, a lithium-ion battery cathode and organic crystals. The richness of these upsampled features admits separation of hard to segment phases, like hairline cracks. We demonstrate that interactive segmentation with these deep features produces high-quality segmentations far faster and with far fewer labels than training or finetuning a more traditional convolutional network.

Neural Cellular Automata for Weakly Supervised Segmentation of White Blood Cells

The detection and segmentation of white blood cells in blood smear images is a key step in medical diagnostics, supporting various downstream tasks such as automated blood cell counting, morphological analysis, cell classification, and disease diagnosis and monitoring. Training robust and accurate models requires large amounts of labeled data, which is both time-consuming and expensive to acquire. In this work, we propose a novel approach for weakly supervised segmentation using neural cellular automata (NCA-WSS). By leveraging the feature maps generated by NCA during classification, we can extract segmentation masks without the need for retraining with segmentation labels. We evaluate our method on three white blood cell microscopy datasets and demonstrate that NCA-WSS significantly outperforms existing weakly supervised approaches. Our work illustrates the potential of NCA for both classification and segmentation in a weakly supervised framework, providing a scalable and efficient solution for medical image analysis.

Segmentation and Classification of Pap Smear Images for Cervical Cancer Detection Using Deep Learning

Cervical cancer remains a significant global health concern and a leading cause of cancer-related deaths among women. Early detection through Pap smear tests is essential to reduce mortality rates; however, the manual examination is time consuming and prone to human error. This study proposes a deep learning framework that integrates U-Net for segmentation and a classification model to enhance diagnostic performance. The Herlev Pap Smear Dataset, a publicly available cervical cell dataset, was utilized for training and evaluation. The impact of segmentation on classification performance was evaluated by comparing the model trained on segmented images and another trained on non-segmented images. Experimental results showed that the use of segmented images marginally improved the model performance on precision (about 0.41 percent higher) and F1-score (about 1.30 percent higher), which suggests a slightly more balanced classification performance. While segmentation helps in feature extraction, the results showed that its impact on classification performance appears to be limited. The proposed framework offers a supplemental tool for clinical applications, which may aid pathologists in early diagnosis.

PathMR: Multimodal Visual Reasoning for Interpretable Pathology Diagnosis

Deep learning based automated pathological diagnosis has markedly improved diagnostic efficiency and reduced variability between observers, yet its clinical adoption remains limited by opaque model decisions and a lack of traceable rationale. To address this, recent multimodal visual reasoning architectures provide a unified framework that generates segmentation masks at the pixel level alongside semantically aligned textual explanations. By localizing lesion regions and producing expert style diagnostic narratives, these models deliver the transparent and interpretable insights necessary for dependable AI assisted pathology. Building on these advancements, we propose PathMR, a cell-level Multimodal visual Reasoning framework for Pathological image analysis. Given a pathological image and a textual query, PathMR generates expert-level diagnostic explanations while simultaneously predicting cell distribution patterns. To benchmark its performance, we evaluated our approach on the publicly available PathGen dataset as well as on our newly developed GADVR dataset. Extensive experiments on these two datasets demonstrate that PathMR consistently outperforms state-of-the-art visual reasoning methods in text generation quality, segmentation accuracy, and cross-modal alignment. These results highlight the potential of PathMR for improving interpretability in AI-driven pathological diagnosis. The code will be publicly available in https://github.com/zhangye-zoe/PathMR.

Towards Comprehensive Cellular Characterisation of H&E slides

Cell detection, segmentation and classification are essential for analyzing tumor microenvironments (TME) on hematoxylin and eosin (H&E) slides. Existing methods suffer from poor performance on understudied cell types (rare or not present in public datasets) and limited cross-domain generalization. To address these shortcomings, we introduce HistoPLUS, a state-of-the-art model for cell analysis, trained on a novel curated pan-cancer dataset of 108,722 nuclei covering 13 cell types. In external validation across 4 independent cohorts, HistoPLUS outperforms current state-of-the-art models in detection quality by 5.2% and overall F1 classification score by 23.7%, while using 5x fewer parameters. Notably, HistoPLUS unlocks the study of 7 understudied cell types and brings significant improvements on 8 of 13 cell types. Moreover, we show that HistoPLUS robustly transfers to two oncology indications unseen during training. To support broader TME biomarker research, we release the model weights and inference code at https://github.com/owkin/histoplus/.