ZMIS-SAM: Segment Anything Model Enhanced with Wavelet Transform for Zooplankton Microscopy Image Instance Segmentation

Plankton monitoring is essential for assessing aquatic ecosystems but is limited by the labor-intensive nature of manual microscopic analysis. Automating the segmentation of plankton from crowded images is crucial, however, it faces two major challenges: (i) the scarcity of pixel-level annotated datasets and (ii) the difficulty of distinguishing plankton from debris and overlapping individuals using conventional CNN-based methods. To address these issues, we propose PlankFormer, a novel framework for plankton instance segmentation. First, to overcome the data shortage, we introduce a method to generate labeled Pseudo Community Images (PCI) by synthesizing individual plankton images onto diverse backgrounds, including those created by generative models. Second, we propose a segmentation model utilizing a Vision Transformer (ViT) backbone with a Mask2Former decoder. To robustly capture the global structural features of plankton against occlusion and debris, we employ a Masked Autoencoder (MAE) for self-supervised pre-training on unlabeled individual images. Experimental results on real-world datasets demonstrate that our method significantly outperforms conventional methods, such as Mask R-CNN, particularly in challenging environments with high debris density. We demonstrate that our synthetic training strategy and MAE-based architecture enable high-precision segmentation with requiring less manual annotations for individual plankton images.

Marine plankton underpin aquatic food webs and play a key role in global CO2 sequestration, making reliable species identification critical for understanding ocean health and climate feedbacks. Existing classification models perform well on individual collections but fail to generalize across instruments and environments due to isolated training datasets and inconsistent labels. To address this, we introduce Planktonzilla-17M, a unified dataset consolidating publicly available plankton image collections spanning thirteen imaging systems. It comprises 17.4 million images with standardized taxonomy and geo-environmental metadata, including 3.74 million plankton images spanning over 602 taxonomic classes, of which 201 are identified at the species level, making it the largest and most comprehensive plankton image dataset to date. Using this large-scale dataset, we perform a controlled comparison between supervised and CLIP-style image--text training on a shared ViT backbone. We find that a supervised classifier matches or exceeds CLIP-style training when trained using taxonomic lineage as text. We further observe that BioCLIP and BioCLIP2 perform poorly on plankton in zero-shot and few-shot settings. Leveraging Planktonzilla-17M improves plankton classification performance, highlighting the limitations of current biological foundation models in marine imaging domains.

The ocean plays a critical role in sustainable development, particularly in climate change mitigation. Among marine ecosystems, blue carbon ecosystems are recognized as important natural carbon sinks. In this context, this paper addresses precise seaweed classification for blue carbon quantification in Ocean Digital Twin initiatives. Conventional methods, including supervised learning (limited by data scarcity and domain gaps) and self-supervised learning (unable to assign class labels), struggle with underwater complexities and diverse seaweed species. To overcome this, we propose a novel two-stage seaweed segmentation technique. This technique first utilizes Supervised and Self-supervised Learning Model Propagation (SSL.Prop.), which leverages supervised learning for initial class information and approximate locations, guiding self-supervised learning for detailed, accurate segmentation. Subsequently, MaskFusion (MF) refines these results by merging instance-level masks for highly accurate segmentation. This integrated approach allows automatic class label assignment and mitigates domain gap effects. Specifically, instance segmentation estimates sparse point locations which then guide self-supervised learning for detailed region segmentation. Evaluated with underwater images from Yamaguchi Prefecture, our full proposed method (SSL.Prop.+MF) achieved a 0.082 mIoU improvement over USIS-SAM, demonstrating significant accuracy gains, particularly for small seaweed. This approach demonstrates strong potential for improving blue carbon quantification and marine ecosystem monitoring.