Manipulation and re-use of images in scientific publications is a growing issue, not only for biomedical publishers, but also for the research community in general. In this work we introduce BINDER - Bio-Image Near-Duplicate Examples Repository, a novel dataset to help researchers develop, train, and test models to detect same-source biomedical images. BINDER contains 7,490 unique image patches for model training, 1,821 same-size patch duplicates for validation and testing, and 868 different-size image/patch pairs for image retrieval validation and testing. Except for the training set, patches already contain manipulations including rotation, translation, scale, perspective transform, contrast adjustment and/or compression artifacts. We further use the dataset to demonstrate how novel adaptations of existing image retrieval and metric learning models can be applied to achieve high-accuracy inference results, creating a baseline for future work. In aggregate, we thus present a supervised protocol for near-duplicate image identification and retrieval without any “real-world” training example. Our dataset and source code are available at hms-idac.github.io/BINDER.