# PlankFormer: Robust Plankton Instance Segmentation via MAE-Pretrained Vision Transformers and Pseudo Community Image Generation

arXiv: https://arxiv.org/abs/2604.17856 · HTML: https://mlsanity.com/paper/2604.17856/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 12 of its 27 references that are in the map.
- First posted on arXiv 20 Apr 2026.

## Builds on (most cited first, 12 of 12)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [Microsoft COCO: Common Objects in Context](https://mlsanity.com/paper/1405.0312/) (2014)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [Mask R-CNN](https://mlsanity.com/paper/1703.06870/) (2017)
- [Masked-attention Mask Transformer for Universal Image Segmentation](https://mlsanity.com/paper/2112.01527/) (2021)
- [An Empirical Study of Training Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.02057/) (2021)
- [Alias-Free Generative Adversarial Networks](https://mlsanity.com/paper/2106.12423/) (2021)
- [Simple Copy-Paste is a Strong Data Augmentation Method for Instance Segmentation](https://mlsanity.com/paper/2012.07177/) (2020)
- [Attention Branch Network: Learning of Attention Mechanism for Visual Explanation](https://mlsanity.com/paper/1812.10025/) (2018)
- [UrFound: Towards Universal Retinal Foundation Models via Knowledge-Guided Masked Modeling](https://mlsanity.com/paper/2408.05618/) (2024)

## Abstract (arXiv)

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.