Accurate plant counting provides valuable information for agriculture such as crop yield prediction, plant density assessment, and phenotype quantification. Vision-based approaches are currently the mainstream solution. Prior art typically uses a detection or a regression model to count a specific plant. However, plants have biodiversity, and new cultivars are increasingly bred each year. It is almost impossible to exhaust and build all species-dependent counting models. Inspired by class-agnostic counting (CAC) in computer vision, we argue that it is time to rethink the problem formulation of plant counting, from what plants to count to how to count plants. In contrast to most daily objects with spatial and temporal invariance, plants are dynamic, changing with time and space. Their non-rigid structure often leads to worse performance than counting rigid instances like heads and cars such that current CAC and open-world detection models are suboptimal to count plants. In this work, we inherit the vein of the TasselNet plant counting model and introduce a new extension, TasselNetV4, shifting from species-specific counting to cross-species counting. TasselNetV4 marries the local counting idea of TasselNet with the extract-and-match paradigm in CAC. It builds upon a plain vision transformer and incorporates novel multi-branch box-aware local counters used to enhance cross-scale robustness. Two challenging datasets, PAC-105 and PAC-Somalia, are harvested. Extensive experiments against state-of-the-art CAC models show that TasselNetV4 achieves not only superior counting performance but also high efficiency.Our results indicate that TasselNetV4 emerges to be a vision foundation model for cross-scene, cross-scale, and cross-species plant counting.

We present a multi-head vision transformer approach for multi-label plant species prediction in vegetation plot images, addressing the PlantCLEF 2025 challenge. The task involves training models on single-species plant images while testing on multi-species quadrat images, creating a drastic domain shift. Our methodology leverages a pre-trained DINOv2 Vision Transformer Base (ViT-B/14) backbone with multiple classification heads for species, genus, and family prediction, utilizing taxonomic hierarchies. Key contributions include multi-scale tiling to capture plants at different scales, dynamic threshold optimization based on mean prediction length, and ensemble strategies through bagging and Hydra model architectures. The approach incorporates various inference techniques including image cropping to remove non-plant artifacts, top-n filtering for prediction constraints, and logit thresholding strategies. Experiments were conducted on approximately 1.4 million training images covering 7,806 plant species. Results demonstrate strong performance, making our submission 3rd best on the private leaderboard. Our code is available at https://github.com/geranium12/plant-clef-2025/tree/v1.0.0.

We describe DS@GT's second-place solution to the PlantCLEF 2025 challenge on multi-species plant identification in vegetation quadrat images. Our pipeline combines (i) a fine-tuned Vision Transformer ViTD2PC24All for patch-level inference, (ii) a 4x4 tiling strategy that aligns patch size with the network's 518x518 receptive field, and (iii) domain-prior adaptation through PaCMAP + K-Means visual clustering and geolocation filtering. Tile predictions are aggregated by majority vote and re-weighted with cluster-specific Bayesian priors, yielding a macro-averaged F1 of 0.348 (private leaderboard) while requiring no additional training. All code, configuration files, and reproducibility scripts are publicly available at https://github.com/dsgt-arc/plantclef-2025.

Early identification of weeds is essential for effective management and control, and there is growing interest in automating the process using computer vision techniques coupled with AI methods. However, challenges associated with training AI-based weed identification models, such as limited expert-verified data and complexity and variability in morphological features, have hindered progress. To address these issues, we present WeedNet, the first global-scale weed identification model capable of recognizing an extensive set of weed species, including noxious and invasive plant species. WeedNet is an end-to-end real-time weed identification pipeline and uses self-supervised learning, fine-tuning, and enhanced trustworthiness strategies. WeedNet achieved 91.02% accuracy across 1,593 weed species, with 41% species achieving 100% accuracy. Using a fine-tuning strategy and a Global-to-Local approach, the local Iowa WeedNet model achieved an overall accuracy of 97.38% for 85 Iowa weeds, most classes exceeded a 90% mean accuracy per class. Testing across intra-species dissimilarity (developmental stages) and inter-species similarity (look-alike species) suggests that diversity in the images collected, spanning all the growth stages and distinguishable plant characteristics, is crucial in driving model performance. The generalizability and adaptability of the Global WeedNet model enable it to function as a foundational model, with the Global-to-Local strategy allowing fine-tuning for region-specific weed communities. Additional validation of drone- and ground-rover-based images highlights the potential of WeedNet for integration into robotic platforms. Furthermore, integration with AI for conversational use provides intelligent agricultural and ecological conservation consulting tools for farmers, agronomists, researchers, land managers, and government agencies across diverse landscapes.

--There has been enormous interest in generative AI since ChatGPT was launched in 2022. However, there are concerns about the accuracy and consistency of the outputs of generative AI. We have carried out an exploratory study on the application of this new technology in research data processing. We identified tasks for which rule-based or traditional machine learning approaches were difficult to apply, and then performed these tasks using generative AI. We demonstrate the feasibility of using the generative AI model Claude 3 Opus in three research projects involving complex data processing tasks: 1) Information extraction: We extract plant species names from historical seedlists (catalogues of seeds) published by botanical gardens. We share the lessons we learnt from these use cases: How to determine if generative AI is an appropriate tool for a given data processing task, and if so, how to maximise the accuracy and consistency of the results obtained. In this paper, we share our insights on the application of generative AI in research software engineering projects. Generative AI can potentially be used to perform a wide variety of research data processing tasks, such as interpreting documents, extracting information from them, and classifying text into categories. Since the tasks are specified through prompts in natural language, the barrier to entry is low. Therefore, this tool can be easily used by domain experts in a wide range of fields, with varying levels of programming skills and depth of knowledge of technical topics such as machine learning.

In our project WatchPlant, we propose to use a decentralized network of living plants as air-quality sensors by measuring their electrophysiology to infer the environmental state, also called phytosensing. We conducted in-lab experiments exposing ivy (Hedera helix) plants to ozone, an important pollutant to monitor, and measured their electrophysiological response. However, there is no well established automated way of detecting ozone exposure in plants. We propose a generic automatic toolchain to select a high-performance subset of features and highly accurate models for plant electrophysiology. Our approach derives plant- and stimulus-generic features from the electrophysiological signal using the tsfresh library. Based on these features, we automatically select and optimize machine learning models using AutoML. We use forward feature selection to increase model performance. We show that our approach successfully classifies plant ozone exposure with accuracies of up to 94.6% on unseen data. We also show that our approach can be used for other plant species and stimuli. Our toolchain automates the development of monitoring algorithms for plants as pollutant monitors. Our results help implement significant advancements for phytosensing devices contributing to the development of cost-effective, high-density urban air monitoring systems in the future.

In this study, we tackle the challenge of identifying plant species from ultra high resolution (UHR) remote sensing images. Our approach involves introducing an RGB remote sensing dataset, characterized by millimeter-level spatial resolution, meticulously curated through several field expeditions across a mountainous region in France covering various landscapes. The task of plant species identification is framed as a semantic segmentation problem for its practical and efficient implementation across vast geographical areas. However, when dealing with segmentation masks, we confront instances where distinguishing boundaries between plant species and their background is challenging. We tackle this issue by introducing a fuzzy loss within the segmentation model. Instead of utilizing one-hot encoded ground truth (GT), our model incorporates Gaussian filter refined GT, introducing stochasticity during training. First experimental results obtained on both our UHR dataset and a public dataset are presented, showing the relevance of the proposed methodology, as well as the need for future improvement.

We present a transfer learning approach using a self-supervised Vision Transformer (DINOv2) for the PlantCLEF 2024 competition, focusing on the multi-label plant species classification. Our method leverages both base and fine-tuned DINOv2 models to extract generalized feature embeddings. We train classifiers to predict multiple plant species within a single image using these rich embeddings. To address the computational challenges of the large-scale dataset, we employ Spark for distributed data processing, ensuring efficient memory management and processing across a cluster of workers. Our data processing pipeline transforms images into grids of tiles, classifying each tile, and aggregating these predictions into a consolidated set of probabilities. Our results demonstrate the efficacy of combining transfer learning with advanced data processing techniques for multi-label image classification tasks.

Phenotypic (or Physical) characteristics of plant species are commonly used to perform clustering. In one of our recent works (Shastri et al. (2021)), we used a probabilistically sampled (using pivotal sampling) and spectrally clustered algorithm to group soybean species. These techniques were used to obtain highly accurate clusterings at a reduced cost. In this work, we extend the earlier algorithm to cluster rice species. We improve the base algorithm in three ways. First, we propose a new function to build the similarity matrix in Spectral Clustering. Commonly, a natural exponential function is used for this purpose. Based upon the spectral graph theory and the involved Cheeger's inequality, we propose the use a base "a" exponential function instead. This gives a similarity matrix spectrum favorable for clustering, which we support via an eigenvalue analysis. Second, the function used to build the similarity matrix in Spectral Clustering was earlier scaled with a fixed factor (called global scaling). Based upon the idea of Zelnik-Manor and Perona (2004), we now use a factor that varies with matrix elements (called local scaling) and works better. Third, to compute the inclusion probability of a specie in the pivotal sampling algorithm, we had earlier used the notion of deviation that captured how far specie's characteristic values were from their respective base values (computed over all species). A maximum function was used before to find the base values. We now use a median function, which is more intuitive. We support this choice using a statistical analysis. With experiments on 1865 rice species, we demonstrate that in terms of silhouette values, our new Sampled Spectral Clustering is 61% better than Hierarchical Clustering (currently prevalent). Also, our new algorithm is significantly faster than Hierarchical Clustering due to the involved sampling.

Scientists from UNSW and Botanic Gardens of Sydney have trained AI to unlock data from millions of plant specimens kept in herbaria around the world, to study and combat the impacts of climate change on flora. "Herbarium collections are amazing time capsules of plant specimens," says lead author on the study, Associate Professor Will Cornwell. "Each year over 8000 specimens are added to the National Herbarium of New South Wales alone, so it's not possible to go through things manually anymore." Using a new machine learning algorithm to process over 3000 leaf samples, the team discovered that contrary to frequently observed interspecies patterns, leaf size doesn't increase in warmer climates within a single species. Published in the American Journal of Botany, this research not only reveals that factors other than climate have a strong effect on leaf size within a plant species, but demonstrates how AI can be used to transform static specimen collections and to quickly and effectively document climate change effects.