Cross-Modality Sub-Image Retrieval using Contrastive Multimodal Image Representations

Eva Breznik, Elisabeth Wetzer, Joakim Lindblad, Nataša Sladoje

In tissue characterization and cancer diagnostics, multimodal imaging has emerged as a powerful technique. Thanks to computational advances, large datasets can be exploited to improve diagnosis and discover patterns in pathologies. However, this requires efficient and scalable image retrieval methods. Cross-modality image retrieval is particularly demanding, as images of the same content captured in different modalities may display little common information. We propose a content-based image retrieval system (CBIR) for reverse (sub-)image search to retrieve microscopy images in one modality given a corresponding image captured by a different modality, where images are not aligned and share only few structures. We propose to combine deep learning to generate representations which embed both modalities in a common space, with classic, fast, and robust feature extractors (SIFT, SURF) to create a bag-of-words model for efficient and reliable retrieval. Our application-independent approach shows promising results on a publicly available dataset of brightfield and second harmonic generation microscopy images. We obtain 75.4% and 83.6% top-10 retrieval success for retrieval in one or the other direction. Our proposed method significantly outperforms both direct retrieval of the original multimodal (sub-)images, as well as their corresponding generative adversarial network (GAN)-based image-to-image translations. We establish that the proposed method performs better in comparison with a recent sub-image retrieval toolkit, GAN-based image-to-image translations, and learnt feature extractors for the downstream task of cross-modal image retrieval. We highlight the shortcomings of the latter methods and observe the importance of equivariance and invariance properties of the learnt representations and feature extractors in the CBIR pipeline. Code will be available at

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