Automatic recognition of protein subcellular location patterns in single cells from immunofluorescence images based on deep learning.

With the improvement of single-cell measurement techniques, there is a growing awareness that individual differences exist among cells, and protein expression distribution can vary across cells in the same tissue or cell line. Pinpointing the protein subcellular locations in single cells is crucial for mapping functional specificity of proteins and studying related diseases. Currently, research about single-cell protein location is still in its infancy, and most studies and databases do not annotate proteins at the cell level. For example, in the human protein atlas database, an immunofluorescence image stained for a particular protein shows multiple cells, but the subcellular location annotation is for the whole image, ignoring intercellular difference. In this study, we used large-scale immunofluorescence images and image-level subcellular locations to develop a deep-learning-based pipeline that could accurately recognize protein localizations in single cells. The pipeline consisted of two deep learning models, i.e. an image-based model and a cell-based model. The former used a multi-instance learning framework to comprehensively model protein distribution in multiple cells in each image, and could give both image-level and cell-level predictions. The latter firstly used clustering and heuristics algorithms to assign pseudo-labels of subcellular locations to the segmented cell images, and then used the pseudo-labels to train a classification model. Finally, the image-based model was fused with the cell-based model at the decision level to obtain the final ensemble model for single-cell prediction. Our experimental results showed that the ensemble model could achieve higher accuracy and robustness on independent test sets than state-of-the-art methods.

Automated identification of protein expression intensity and classification of protein cellular locations in mouse brain regions from immunofluorescence images.

Knowledge of protein expression in mammalian brains at regional and cellular levels can facilitate understanding of protein functions and associated diseases. As the mouse brain is a typical mammalian brain considering cell type and structure, several studies have been conducted to analyze protein expression in mouse brains. However, labeling protein expression using biotechnology is costly and time-consuming. Therefore, automated models that can accurately recognize protein expression are needed. Here, we constructed machine learning models to automatically annotate the protein expression intensity and cellular location in different mouse brain regions from immunofluorescence images. The brain regions and sub-regions were segmented through learning image features using an autoencoder and then performing K-means clustering and registration to align with the anatomical references. The protein expression intensities for those segmented structures were computed on the basis of the statistics of the image pixels, and patch-based weakly supervised methods and multi-instance learning were used to classify the cellular locations. Results demonstrated that the models achieved high accuracy in the expression intensity estimation, and the F1 score of the cellular location prediction was 74.5%. This work established an automated pipeline for analyzing mouse brain images and provided a foundation for further study of protein expression and functions.