Automated detection of fluorescent cells in in‐resin fluorescence sections for integrated light and electron microscopy

Summary Integrated array tomography combines fluorescence and electron imaging of ultrathin sections in one microscope, and enables accurate high‐resolution correlation of fluorescent proteins to cell organelles and membranes. Large numbers of serial sections can be imaged sequentially to produce aligned volumes from both imaging modalities, thus producing enormous amounts of data that must be handled and processed using novel techniques. Here, we present a scheme for automated detection of fluorescent cells within thin resin sections, which could then be used to drive automated electron image acquisition from target regions via ‘smart tracking’. The aim of this work is to aid in optimization of the data acquisition process through automation, freeing the operator to work on other tasks and speeding up the process, while reducing data rates by only acquiring images from regions of interest. This new method is shown to be robust against noise and able to deal with regions of low fluorescence. Lay description Integrated Light and Electron Microscopy is a recent technique, which uses a light microscope inside an electron microscope to analyse the position of molecules in cells and tissues. The resulting data can give clues about the functions of those molecules in health and disease. However, this technique can produce huge amounts of image data, which has to be stored and analysed by scientists, with high computational and time costs. To streamline the process, we have designed a method whereby computers can automatically detect the position of the molecules of interest, using fluorescent labels, so that electron images are only acquired from these target regions. This method will form part of a workflow to automate the process of data collection, freeing scientists to work on other tasks.