Z-stack Depth Colorcode ImageJ FIJI plugin

ExTrack MLE for diffusive noisy single-particle tracks

This is a plugin for ImageJ2 for multifractal analysis of 2D and 3D images. Cite: MULTIFRAC: An ImageJ plugin for multiscale characterization of 2D and 3D stack images . IG Torre, R. J. Heck and AM Tarquis. SoftwareX, 12, 100574.

An ImageJ plugin to quantify ciliary shape, length, and fluorescence.

An ImageJ plugin to analyze the flagellar beat of sperm, motile cilia beat, and sperm steering.

A simple toolbox of ImageJ plugins for quantifying adipocyte morphology and function in tissues and in vitro.

spatial and temporal cross correlations in 1D and 2D for fluorescent microscopy (ImageJ plugin)

A toolbox to analyze spherical and filamentous objects in multifocal images with high precision.

Scripts for executing Fiji plugin BoneJ in headless mode in Python to compute bone microstructure metrics

😎 Awesome lists about ImageJ Plugins!

Fiji/ImageJ plugin to annotate a labeled image

Fiji/ImageJ plugin to help measuring linear distances.

ImageJ-plugin that performs standard analysis of colony formation assays conducted in 6- to 24-well dishes.

ImageJ plugin to quickly load multiphoton imaging data from PrairieView folders

Mageek is an ImageJ Java plugin to batch process microscope images

ImageJ plugin that converts regions from label maps into polygons

An ImageJ plugin to prepare images for analysis using CiliaQ.

Package for animal pattern analysis, with machine learning for MICA Toolbox (beta)

ExtractSharpestPlane_JNH is an ImageJ/FIJI plugin to automatically extract the sharpest plane by highest SD from image stacks for large data sets.