MorphoLibJ is a collection of mathematical morphology methods and plugins for ImageJ (morphological filtering/reconstruction, watershed segmentation, 2D/3D measurements, binary/label images utilities).
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).
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.
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.
NanoJ is an open-source toolbox for super-resolution microscopy data analysis. It encompasses several essential processing steps; spatiotemporal alignment of raw data (NanoJ-Core), super-resolution image reconstruction (NanoJ-SRRF), image quality assessment (NanoJ-SQUIRREL), structural modelling (NanoJ-VirusMapper) and control of the sample environment (NanoJ-Fluidics).
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.
