Electron microscopes have been used for decades to image cellular detail at high magnification. However the resulting images are 2‐dimensional. The development of an electron microscope in which we can section tissue in situ means that we can now acquire stacks of images giving us detail in 3‐dimensions. However the challenge with these large datasets is to reconstruct features of interest to form a 3D model. There are a number of computer programs that can be used to do this but they are not intuitive and can be overwhelming for researchers new to them. Here we explain terminology used in the programs and provide a step‐by‐step guide with accompanying videos to help researchers get started with their image analysis and get the best from their data.
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