NIH ImageJ

HyperSpy is an open-source Python library that provides tools to facilitate the interactive data analysis of multi-dimensional datasets that can be described as multi-dimensional arrays of a given signal.

MicrobeJ is an analysis platform specifically built for automated analysis of the most common intensity, morphological and spatiotemporal measurements from bacterial datasets. MicrobeJ enables customised detection of unique features, is optimised for high-throughput, and has a rich user interaction.

OpenPNM is an open-source pore network modelling package providing for a wide variety of pore-scale simulation tasks. It is designed to be fully agnostic to the topology and dimensionality of network by using graph theory representations to describe the architecture.

MorphoLibJ is a collection of mathematical morphology methods and plugins for ImageJ (morphological filtering/reconstruction, watershed segmentation, 2D/3D measurements, binary/label images utilities).

Microscopy Image Browser (MIB) is a package for image processing, segmentation, and visualisation of multi-dimensional (2D-4D) microscopy datasets.

TRABI (temporal, radial-aperture-based intensity estimation) is a free ImageJ macro used for 3D processing of 2D single molecule microscopy data. Through intensity estimation in different regions of the emission pattern of single fluorophores, a relative 3D position can be determined from 2D data with no adaptation to the microscope.