Dnq2025/Mask2former_Finetune

MicroStructFormer EM Ultrastructure Dataset

This dataset repository contains the electron microscopy (EM) images and their corresponding semantic segmentation masks used for training and fine-tuning the MicroStructFormer model.

Dataset Description

The dataset is specifically annotated for the segmentation of critical ultrastructural elements in gene-edited mouse models:

• Abnormalities
• Mitochondria (and mitochondria-like organelles)
• Periaxonal Space

For an interactive inference demo, comprehensive documentation, and the full pipeline integration guide, please visit our Official Project Website.

Dataset Use, License, and Citation

This Hugging Face dataset repository is associated with the following bioRxiv preprint:

Deng N, Miao G, Khadra A, Peterson AC, Bagheri H. Deep learning-based decoding of axonal ultrastructure in gene-edited mice using electron microscopy imaging. bioRxiv. 2026. DOI: 10.64898/2026.05.26.727755.

These data and associated annotations are provided for non-commercial academic and research use under the CC-BY-NC-SA 4.0 license selected for this repository. Users must provide appropriate attribution to the original authors and cite the associated preprint when using this dataset, annotations, derived measurements, or any models trained from this project in publications, preprints, theses, presentations, software repositories, benchmarks, or derivative analyses.

Use of this dataset for commercial purposes is not permitted without prior written permission from the authors. Any redistributed or modified version of this dataset, annotations, or derived dataset variants must preserve attribution to the original authors and must be shared under the same or a compatible non-commercial share-alike license, unless separate written permission is obtained from the authors.

Users must not claim ownership of the original images, annotations, Hugging Face dataset versions, or associated derived resources.

Please cite our preprint if you use this dataset in your research:

@article {Deng2026.05.26.727755,
    author = {Deng, Nianqi and Miao, Guillaume and Khadra, Anmar and Peterson, Alan C and Bagheri, Hooman},
    title = {Deep learning-based decoding of axonal ultrastructure in gene-edited mice using electron microscopy imaging},
    elocation-id = {2026.05.26.727755},
    year = {2026},
    doi = {10.64898/2026.05.26.727755},
    publisher = {Cold Spring Harbor Laboratory},
    journal = {bioRxiv}
}