Going Beyond U-Net: Assessing Vision Transformers for Semantic Segmentation in Microscopy Image Analysis

Segmentation is a crucial step in microscopy image analysis. Numerous approaches have been developed over the past years, ranging from classical segmentation algorithms to advanced deep learning models. While U-Net remains one of the most popular and well-established models for biomedical segmentation tasks, recently developed transformer-based models promise to enhance the segmentation process of microscopy images. In this work, we assess the efficacy of transformers, including UNETR, the Segment Anything Model, and Swin-UPerNet, and compare them with the well-established U-Net model across various image modalities such as electron microscopy, brightfield, histopathology, and phase-contrast. Our evaluation identifies several limitations in the original Swin Transformer model, which we address through architectural modifications to optimise its performance. The results demonstrate that these modifications improve segmentation performance compared to the classical U-Net model and the unmodified Swin-UPerNet. This comparative analysis highlights the promise of transformer models for advancing biomedical image segmentation. It demonstrates that their efficiency and applicability can be improved with careful modifications, facilitating their future use in microscopy image analysis tools.

BPE Gets Picky: Efficient Vocabulary Refinement During Tokenizer Training

Language models can largely benefit from efficient tokenization. However, they still mostly utilize the classical BPE algorithm, a simple and reliable method. This has been shown to cause such issues as under-trained tokens and sub-optimal compression that may affect the downstream performance. We introduce Picky BPE, a modified BPE algorithm that carries out vocabulary refinement during tokenizer training. Our method improves vocabulary efficiency, eliminates under-trained tokens, and does not compromise text compression. Our experiments show that our method does not reduce the downstream performance, and in several cases improves it.

SwinIA: Self-Supervised Blind-Spot Image Denoising with Zero Convolutions

The essence of self-supervised image denoising is to restore the signal from the noisy image alone. State-of-the-art solutions for this task rely on the idea of masking pixels and training a fully-convolutional neural network to impute them. This most often requires multiple forward passes, information about the noise model, and intricate regularization functions. In this paper, we propose a Swin Transformer-based Image Autoencoder (SwinIA), the first convolution-free architecture for self-supervised denoising. It can be trained end-to-end with a simple mean squared error loss without masking and does not require any prior knowledge about clean data or noise distribution. Despite its simplicity, SwinIA establishes state-of-the-art on several common benchmarks.