Million-scale multimodal pollen microscopy with expert-guided foundation models
Authors: András Biricz, Björn Gedda, Donát Magyar, Antonio Spanu, János Fillinger, Péter Pollner, István Csabai
Organizations: Department of Physics of Complex Systems, ELTE Eötvös Lor´and University, Budapest, Hungary · 2The Palynological Laboratory at the Swedish Museum of Natural History, Stockholm, Sweden · 3National Centre for Public Health and Pharmacy, Budapest, Hungary · 4INRAE, UR 546 BioSP, Site Agroparc, Avignon 84914, France · 5National Kor´anyi Institute for Pulmonology, Budapest, Hungary · 6Health Data Science and AI Knowledge Centre, Health Services Management Training Centre, Faculty of Health and Public Administration, Semmelweis University, Budapest, Hungary · Department of Biological Physics, ELTE Eötvös Lor´and University, Budapest, Hungary
Abstract
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.
Traditional melissopalynology is a time-consuming and subjective process, often taking 4-6 hours per sample. We present an automated, high-throughput microscopy system that integrates H∞ robust mechanical control with advanced deep learning pipelines for the precise counting, classification, and morphological analysis of pollen grains from Bio Bio region in south central territory in Chile. Our system employs U2-Net for salient object detection and a DINOv2 Vision Transformer backbone trained via Deep Metric Learning for classification. By integrating Gradient-Weighted Attention, the model provides human-interpretable texture and diagnostic feature annotations. The system achieves a 95.8% classification recall and a 6x processing speedup compared to manual expert analysis.
Precision weed control requires species-level identification and instance-level localization. However, conventional object detectors use a closed vocabulary, limiting their deployment across regions, and cannot explain their predictions in complex agricultural scenes. Multimodal large language models (MLLMs) offer visual grounding and reasoning capabilities, but insufficient botanical knowledge can cause hallucinations in fine-grained weed identification. This study introduces WeedExpert-R1, a multimodal model that learns visually grounded botanical reasoning through verifiable rewards. A domain-specific Chain-of-Thought synthesis pipeline combines a human-curated botanical trait dictionary with an Auditor-Synthesizer LLM workflow to generate reasoning data for supervised fine-tuning. Group Relative Policy Optimization is then applied with rewards for format, accuracy, instance count, and response length. Across 37 weed species from six datasets, WeedExpert-R1-4B achieved 75.82 percent exact-set precision at an IoU threshold of 0.5, 89.30 percent precision, and 87.81 percent recall. It outperformed proprietary models, including GPT-5.4 and Gemini-3.1-Pro, and larger open-source models, including Qwen3-VL-30B-Instruct and Gemma-4-31B-it. Results on unseen species further demonstrate its open-vocabulary capability and potential for deployment across diverse regions and crops without retraining.
Microscopic imaging provides essential visual evidence for studying plant biology and pathology at the cellular and subcellular levels. However, existing benchmarks on vision-language models primarily focus on macroscopic plant imagery, while the microscopic domain remains underexplored. To address this gap, we present PlantMicro, a comprehensive benchmark for evaluating vision-language models (VLMs) in microscopic plant imagery. PlantMicro integrates more than 5,000 images collected across diverse hosts, biological domains, and imaging modalities. Building on this diversity, we design a set of complementary tasks that capture different facets of microscopic image understanding. To support these tasks, we construct over 9,000 VQA pairs that systematically evaluate the capabilities of VLMs. Experiments on PlantMicro show that current VLMs struggle with fine-grained recognition and biologically grounded reasoning. For example, GPT-5 achieves 34.93% accuracy on the pathogen classification task, which is only modestly above the random-guessing baseline. The results highlight a significant gap in current VLMs' ability to comprehend plant microscopic images. PlantMicro provides a standardized foundation for advancing VLMs toward reliable and comprehensive microscopy-level plant understanding.