MicrobeJ

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.

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).

Collection of Fiji macros to automate the boring stuff: batch process all files in a folder and save them by converting from .czi images (Bioformats) to .tif format; save all open images in .tif format in an output folder of choice; batch process all .tif files in a folder and save 3 channels separately; apply local contrast enhancement (CLAHE) to a Z-stack; batch segmentation of cell nuclei (or other blob-like objects) in fluorescence images by auto-thresholding.

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.