TileBac: A Benchmark CryoEM Dataset of Bacteria in Ultralow-Dose Montage Tiles

Abstract

Current segmentation models are capable of routine identification of biological features in noisy cryogenic electron microscopy (cryoEM) images. However, there are still challenges with complete segmentation of high boundary, thin objects such as bacterial cell envelopes and flagella. Moreover, ultralow-dose cryoEM images pose as an additional challenge to boundary distinctions between the object and background. Here, we present TileBac, a benchmark dataset of ultralow-dose montage tiles of Pantoea sp. YR343 to segment bacterial inner and outer membranes for evaluation of model effectiveness. We show that foundation models outperform convolutional neural networks at continuous bacterial cell envelope segmentation despite having lower performance metrics. We release the TileBac benchmark dataset on Hugging Face for further insights into model architecture development.