Restoring Fluorescence Microscopy Images by Transfer Learning From Tailored Data

Abstract

In fluorescence microscopy imaging, noise is a very usual phenomenon. To some extent, it can be suppressed by increasing the amount of the photon exposure; however, it is not preferable since this may not be tolerated by the subjected specimen. Thus, a sophisticated computational method is needed to denoise each acquired micrograph, so that they become more adequate for further feature extraction and image analysis. However, apart from the difficulties of the denoising problem itself, one main challenge is that the absence of the ground-truth images makes the data-driven techniques less applicable. In order to tackle this challenge, we suggest to tailor a dataset by handpicking images from unrelated source datasets. Our tailoring strategy involves exploring some low-level view-based features of the candidate images, and their similarities to those of the fluorescence microscopy images. We pretrain and fine-tune the well-known feed-forward denoising convolutional neural networks (DnCNNs) on our tailored dataset and a very limited amount of fluorescence images, respectively to ensure both the diversity and the content-awareness. The quantitative and visual experimentation show that our approach is able to curate a dataset, which is significantly superior to the arbitrarily chosen source images, and well-approximates to the fluorescence images. Moreover, the combination of the tailored dataset with a few fluorescence data through the use of fine-tuning offers a good balance between the generalization capability and the content-awareness, on the majority of considered scenarios.