HyperSpy

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.

py4DSTEM is a Python toolkit for analysis and visualisation of 4D-STEM data.

abTEM is a pure Python code for running simulations of (scanning) transmission electron microscopy images using the multi -slice or PRISM algorithms. It is open-source, blazing fast, and extremely versatile and easy to extend.

IPyvolume is a Python library to visualise 3D volumes and glyphs (e.g., 3D scatter plots), in Jupyter notebooks with minimal configuration and effort.

DECODE is a Python and Pytorch based deep learning tool for high density 3D single molecule localisation microscopy (SMLM) analysis.

StarDist is an AI-based tool for object detection with star-convex shapes in 2D and 3D. Intended for cell nuclei detection/segmentation in microscopy images, it can be used via the stand-alone Python software package, or with the provided plugins for other common image analysis software suites (e.g., Fiji, napari, QuPath).