TrackPy is a Python package for particle tracking in 2D, 3D and higher dimensions. It can be used at a range of length scales and applied to image stacks recorded using both light microscopy and electron microscopy.
Prismatic is a CUDA/C++/Python GPU+CPU software package for fast image simulation in high resolution and scanning transmission electron microscopy (HRTEM & STEM) that includes a graphic user interface.
SR-Tesseler is an open-source interactive single molecule localisation microscopy clustering tool based on Voronoï tesselation, that allows for segmentation and quantification of localisation-based super-resolution microscopy data.
PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images. The pipeline is tuned for images acquired with confocal and light sheet microscopy and can be used to segment both plant and animal tissues.