DEMIS: Electron Microscopy Image Stitching Using Deep Learning Features and Global Optimisation

Petr Šilling, Michal Španěl

2025

Abstract

Accurate stitching of overlapping image tiles is essential for reconstructing large-scale Electron Microscopy (EM) images during Whole Slide Imaging. Current stitching approaches rely on handcrafted features and translation-only global alignment based on Minimum Spanning Tree (MST) construction. This results in suboptimal global alignment since it neglects rotational errors and works only with transformations estimated from pairwise feature matches, discarding valuable information tied to individual features. Moreover, handcrafted features may have trouble with repetitive textures. Motivated by the limitations of current methods and recent advancements in deep learning, we propose DEMIS, a novel EM image stitching method. DEMIS uses Local Feature TRansformer (LoFTR) for image matching, and optimises translational and rotational parameters directly at the level of individual features. For evaluation and training, we create EM424, a synthetic dataset generated by splitting high-resolution EM images into arrays of overlapping image tiles. Furthermore, to enable evaluation on unannotated real-world data, we design a no-reference stitching quality metric based on optical flow. Experiments that use the new metric show that DEMIS can improve the average results from 32.11 to 2.28 compared to current stitching techniques (a 1408% improvement). Code is available at: https://github.com/PSilling/demis.

Paper Citation

in Harvard Style

Šilling P. and Španěl M. (2025). DEMIS: Electron Microscopy Image Stitching Using Deep Learning Features and Global Optimisation. In Proceedings of the 18th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 1: BIOIMAGING; ISBN 978-989-758-731-3, SciTePress, pages 255-265. DOI: 10.5220/0013314900003911

in Bibtex Style

@conference{bioimaging25,
author={Petr Šilling and Michal Španěl},
title={DEMIS: Electron Microscopy Image Stitching Using Deep Learning Features and Global Optimisation},
booktitle={Proceedings of the 18th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 1: BIOIMAGING},
year={2025},
pages={255-265},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0013314900003911},
isbn={978-989-758-731-3},
}

in EndNote Style

TY - CONF

JO - Proceedings of the 18th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 1: BIOIMAGING
TI - DEMIS: Electron Microscopy Image Stitching Using Deep Learning Features and Global Optimisation
SN - 978-989-758-731-3
AU - Šilling P.
AU - Španěl M.
PY - 2025
SP - 255
EP - 265
DO - 10.5220/0013314900003911
PB - SciTePress