SimSearch: A Human-in-The-Loop Learning Framework for Fast Detection of Regions of Interest in Microscopy Images

Objective: Large-scale microscopy-based experiments often result in images with rich but sparse information content. An experienced microscopist can visually identify regions of interest (ROIs), but this becomes a cumbersome task with large datasets. Here we present SimSearch, a framework for quick and easy user-guided training of a deep neural model aimed at fast detection of ROIs in large-scale microscopy experiments. Methods: The user manually selects a small number of patches representing different classes of ROIs. This is followed by feature extraction using a pre-trained deep-learning model, and interactive patch selection pruning, resulting in a smaller set of clean (user approved) and larger set of noisy (unapproved) training patches of ROIs and background. The pre-trained deep-learning model is thereafter first trained on the large set of noisy patches, followed by refined training using the clean patches. Results: The framework is evaluated on fluorescence microscopy images from a large-scale drug screening experiment, brightfield images of immunohistochemistry-stained patient tissue samples, and malaria-infected human blood smears, as well as transmission electron microscopy images of cell sections. Compared to state-of-the-art and manual/visual assessment, the results show similar performance with maximal flexibility and minimal a priori information and user interaction. Conclusions: SimSearch quickly adapts to different data sets, which demonstrates the potential to speed up many microscopy-based experiments based on a small amount of user interaction. Significance: SimSearch can help biologists quickly extract informative regions and perform analyses on large datasets helping increase the throughput in a microscopy experiment.