Many scientific imaging applications, especially microscopy, can produce terabytes of data per day. These applications can benefit from recent advances in computer vision and deep learning. In our work with biologists on robotic microscopy applications (e.g., to distinguish cellular phenotypes) we've learned that assembling high quality image datasets that separate signal from noise is a difficult but important task. We've also learned that there are many scientists who may not write code, but who are still excited to utilize deep learning in their image analysis work. A particular challenge we can help address involves dealing with out-of-focus images. Even with the autofocus systems on state-of-the-art microscopes, poor configuration or hardware incompatibility may result in image quality issues. Having an automated way to rate focus quality can enable the detection, troubleshooting and removal of such images.

Deep Learning to the Rescue
In “Assessing Microscope Image Focus Quality with Deep Learning”, we trained a deep neural network to rate the focus quality of microscopy images with higher accuracy than previous methods. We also integrated the pre-trained TensorFlow model with plugins in Fiji (ImageJ) and CellProfiler, two leading open source scientific image analysis tools that can be used with either a graphical user interface or invoked via scripts.