cisTEM is user-friendly software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them. Comprising a number of tools to process image data including movies, micrographs and stacks of single-particle images, cisTEM implements a complete pipeline of cryo-EM processing steps. It is developed and maintained by the laboratory of Tim Grant (Morgridge Institute for Research), who along with Nikolaus Grigorieff (UMass Chan Medical School) and Alexis Rohou first developed the software at the Janelia Research Campus. cisTEM is distributed under the Janelia Research Campus Software License and can be downloaded here. We recommend downloading and using the pre-compiled binaries, rather than compiling the source code, for best performance. New users are encouraged to follow the tutorial, which provides a quick way to become familiar with the most important functions of cisTEM.