Dataset for Top Model Decision Tree: Selecting Segmentation Models for Reliable Quantitative Analysis in Low- and Ultralow-Dose CryoEM

Abstract

Motivation Multiple deep learning model architectures can be used to segment bacterial membranes in cryoEM images. However, an AI-based tool advancement is often presented with only a single segmentation model for broad use, and this single model may show inconsistent results across datasets from different users. Here, we present the Top Model Decision Tree, a model screening framework to screen for the best model to generate bacterial inner and outer membrane masks based on user priorities. We use pre-trained segmentation models from YOLOv11, YOLO26, U-Net, Detectron2 and SAM3 fine-tuned on bacterial inner and outer membranes imaged with cryoEM. Run the Framework This notebook must be opened in Google Colab. Mount Google Drive and run with a GPU-based runtime. Open the notebook and follow steps to git clone in folders and files within this repository. There will be a repeating top_model_decision_tree.ipynb (notebook clone) that will not be used. Save your .png binary mask files and .csv table outputs within your Google Drive or download before closing the notebook. The models and all analysis/training scripts are available at [GitHub: https://github.com/Lynnicia/CryoEM_membranes_top_model_decision_tree and https://github.com/Sireesiru/Semantic-Segmentation-of-bacterial-cell-envelope-using-U-Nets.