Optical microscopy is one of the most widely used techniques in research studies for life sciences and biomedicine. These applications require reliable experimental pipelines to extract valuable knowledge from the measured samples and must be supported by image quality assessment (IQA) to ensure correct processing and analysis of the image data. IQA methods are implemented with variable complexity. However, while most quality metrics have a straightforward implementation, they might be time consuming and computationally expensive when evaluating a large dataset. In addition, quality metrics are often designed for well-defined image features and may be unstable for images out of the ideal domain. To overcome these limitations, recent works have proposed deep learning-based IQA methods, which can provide superior performance, increased generalizability and fast prediction. Our method, named $\mathrmμ$DeepIQA, is inspired by previous studies and applies a deep convolutional neural network designed for IQA on natural images to optical microscopy measurements. We retrained the same architecture to predict individual quality metrics and global quality scores for optical microscopy data. The resulting models provide fast and stable predictions of image quality by generalizing quality estimation even outside the ideal range of standard methods. In addition, $\mathrmμ$DeepIQA provides patch-wise prediction of image quality and can be used to visualize spatially varying quality in a single image. Our study demonstrates that optical microscopy-based studies can benefit from the generalizability of deep learning models due to their stable performance in the presence of outliers, the ability to assess small image patches, and rapid predictions.