Fully Unsupervised Annotation of C. Elegans

In this work we present a novel approach for unsupervised multi-graph matching, which applies to problems for which a Gaussian distribution of keypoint features can be assumed. We leverage cycle consistency as loss for self-supervised learning, and determine Gaussian parameters through Bayesian Optimization, yielding a highly efficient approach that scales to large datasets. Our fully unsupervised approach enables us to reach the accuracy of state-of-the-art supervised methodology for the use case of annotating cell nuclei in 3D microscopy images of the worm C. elegans. To this end, our approach yields the first unsupervised atlas of C. elegans, i.e. a model of the joint distribution of all of its cell nuclei, without the need for any ground truth cell annotation. This advancement enables highly efficient annotation of cell nuclei in large microscopy datasets of C. elegans. Beyond C. elegans, our approach offers fully unsupervised construction of cell-level atlases for any model organism with a stereotyped cell lineage, and thus bears the potential to catalyze respective comparative developmental studies in a range of further species.

Unlocking the Potential of Operations Research for Multi-Graph Matching

We consider the incomplete multi-graph matching problem, which is a generalization of the NP-hard quadratic assignment problem for matching multiple finite sets. Multi-graph matching plays a central role in computer vision, e.g., for matching images or shapes, so that a number of dedicated optimization techniques have been proposed. While the closely related NP-hard multi-dimensional assignment problem (MDAP) has been studied for decades in the operations research community, it only considers complete matchings and has a different cost structure. We bridge this gap and transfer well-known approximation algorithms for the MDAP to incomplete multi-graph matching. To this end, we revisit respective algorithms, adapt them to incomplete multi-graph matching, and propose their extended and parallelized versions. Our experimental validation shows that our new method substantially outperforms the previous state of the art in terms of objective and runtime. Our algorithm matches, for example, 29 images with more than 500 keypoints each in less than two minutes, whereas the fastest considered competitor requires at least half an hour while producing far worse results.