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Scanning precession electron diffraction (SPED) enables the local crystallography of materials to be probed on the nanoscale by recording a two-dimensional precession electron diffraction (PED) pattern at every probe position as a dynamically rocking electron beam is scanned across the specimen. SPED data from nanocrystalline materials commonly contain some PED patterns in which diffraction is measured from multiple crystals. To analyse such data, it is important to perform nanocrystal segmentation to isolate both the location of each crystal and a corresponding representative diffraction signal. This also reduces data dimensionality significantly. Here, two approaches to nanocrystal segmentation are presented, the first based on virtual dark-field imaging and the second on non-negative matrix factorization. Relative merits and limitations are compared in application to SPED data obtained from partly overlapping nanoparticles, and particular challenges are highlighted associated with crystals exciting the same diffraction conditions. It is demonstrated that both strategies can be used for nanocrystal segmentation without prior knowledge of the crystal structures present, but also that segmentation artefacts can arise and must be considered carefully. The analysis workflows associated with this work are provided open-source. LAY DESCRIPTION: Scanning precession electron diffraction is an electron microscopy technique that enables studies of the local crystallography of a broad selection of materials on the nanoscale. The technique involves the acquisition of a two-dimensional diffraction pattern for every probe position in an area of the sample. The four-dimensional dataset collected by this technique can typically comprise up to 500 000 diffraction patterns. For nanocrystalline materials, it is common that single diffraction patterns contain signals from overlapping crystals. To process such data, we use nanocrystal segmentation, where a representative diffraction pattern is constructed for each individual crystal, together with a real space image showing its morphology and location in the data. This reduces the dimensionality of the data and allows unmixing of signals from overlapping crystals. In this work, we demonstrate two methods for nanocrystal segmentation, one based on creating virtual dark-field images, and one based on unsupervised machine learning. A model system of partly overlapping nanoparticles is used to demonstrate the segmentation, and a demanding case for segmentation is highlighted, where some crystals are not discernible based on their diffraction patterns. To obtain a more complete nanocrystal segmentation, we add an image segmentation routine to both methods, and we discuss benefits and limitations of the two methods. The demonstration data and the used code are provided open-source, so that it can be used by everyone for analysis of nanocrystalline materials or as a starting point for further development of nanocrystal segmentation in scanning precession electron diffraction data., (© 2019 The Authors. Journal of Microscopy published by John Wiley & Sons Ltd on behalf of Royal Microscopical Society.)