Automated Palynological Analysis System: Integrating Deep Metric Learning and U^{2}-Net Detection in H\infty bright field microscopy

Automated pollen identification from microscopy remains a bottleneck in aerobiology, palaeoecology and biodiversity monitoring, because scalable systems must generalise across specimen preparation, scanner settings and geographic origins while retaining palynological interpretability. To address this gap, we present a million-scale multimodal pollen microscopy resource, Pollen AI Atlas, assembled from pure-species whole-slide bright-field images spanning four geographic origins, four scanner settings and 46 taxon labels across 31 botanical families. Seeded by one manually selected exemplar per source slide, token-level mining and filtering produced 1,511,390 released grain detections with 99.6% proposal precision in expert-curated test regions. Each detection was paired with machine-generated grain-level morphological captions from five open-weight vision-language models, guided by expert-verified palynological anchors, yielding structured descriptions of aperture systems, wall ornamentation, shape and size. Among the evaluated models, Gemma4 provided the most controlled primary caption set, combining tight length control, no leakage and the strongest text-retrieval performance. Baseline benchmarks with frozen visual features reached 88.16% top-1 accuracy, while cross-regional retrieval showed that caption-derived text embeddings remained robust when image similarity degraded (mAP@20 0.811 versus 0.262). Released data, annotations, captions, splits, code, and weights provide a benchmark for pollen recognition, cross-regional domain adaptation and domain-specific multimodal microscopy learning.

Analyzing microscopy images to extract biological object properties (e.g., their morphological organization, temporal dynamics, and population density) is fundamental to various biomedical research. Yet conducting this manually is costly and time-consuming. Though deep learning-based approaches have been explored to automate this process, the substantial diversity of microscopy analysis settings in practice (including variations of biological object types, sample processing protocols, imaging equipment, and analysis tasks, etc.) often renders them ineffective. As a result, these approaches typically require extensive adaptation for different settings, which, however, can impose burdens that are often practically unsustainable for laboratories, forcing biomedical researchers to still commonly rely on manual analysis, thereby severely bottlenecking the pace of biomedical research progress. This situation has created a pressing and long-standing need for a reliable and broadly applicable microscopy image analysis tool, yet such a tool is still missing. To address this gap, we present the first ready-to-use microscopy image analysis framework, MicroscopyMatching, that can reliably perform key analysis tasks (including segmentation, tracking, and counting) across diverse microscopy analysis settings. From a fundamentally different perspective, MicroscopyMatching reformulates diverse microscopy image analysis tasks as a unified matching problem, effectively handling this problem by exploiting the robust matching capability from pre-trained latent diffusion models.

Extracting standardized metallurgical metrics from microscopy images remains challenging due to complex grain morphology and the data demands of supervised segmentation. To bridge foundational computer vision with practical metallurgical evaluation, we propose an automated pipeline for dense instance segmentation and grain size estimation that adapts Cellpose-SAM to microstructures and integrates its topology-aware gradient tracking with an ASTM E112 Jeffries planimetric module. We systematically benchmark this pipeline against a classical convolutional network (U-Net), an adaptive-prompting vision foundation model (MatSAM) and a contemporary vision-language model (Qwen2.5-VL-7B). Our evaluations reveal that while the out-of-the-box vision-language model struggles with the localized spatial reasoning required for dense microscopic counting and MatSAM suffers from over-segmentation despite its domain-specific prompt generation, our adapted pipeline successfully maintains topological separation. Furthermore, experiments across progressively reduced training splits demonstrate exceptional few-shot scalability; utilizing only two training samples, the proposed system predicts the ASTM grain size number (G) with a mean absolute percentage error (MAPE) as low as 1.50%, while robustness testing across varying target grain counts empirically validates the ASTM 50-grain sampling minimum. These results highlight the efficacy of application-level foundation model integration for highly accurate, automated materials characterization. Our project repository is available at https://github.com/mueez-overflow/ASTM-Grain-Size-Estimator.