pyxem is an open-source Python library for multi-dimensional diffraction microscopy. It has been primarily developed as a platform for hybrid diffraction-microscopy based on 4D scanning diffraction microscopy data in which a 2D diffraction pattern is recorded at every position in a 2D scan of a specimen.
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.
AFT is an open-source workflow to quantify alignment of fibrillar features in bioimages. It allows for evaluation of alignment lengthscale and works with a number of different imaging modalities.
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.
