TrackMate is your buddy for your everyday tracking.

The U-Net Segmentation plugin for Fiji (ImageJ)

FIJI plugin for tracing of curvilinear structures in volumetric microscopy datasets

Z-stack Depth Colorcode ImageJ FIJI plugin

A Fiji/ImageJ plugin to generate ROIs from label images, allowing ROI erosion and quantification

Plugins for bone image analysis

Curve tracing ImageJ plugin

ImageJ convenience layer for N5

Detection of Molecules plugin for ImageJ, Utrecht University

A Fiji plugin that automatically quantify synapses from multi-channel fluorescence microscopy images.

ImageJ plugin detecting and colocalizing particles of given size (vesicles, dots, etc on biological microscopy images)

Modular, object-based analysis for ImageJ/Fiji

🔬 This is an ImageJ or Fiji plugin to identify, characterize, quantify and classify cells according to user-defined conditions.

Fiji / ImageJ plugin for Imaging Alignment. This plugin manages two types of alignment: Manual Alignment and Automatic Alignment.

A plugin to combine power of mouse and keyboard control with image processing and analysis tools in ImageJ

ImageJ scripts for stereology and morphometry

ImageJ plugin reading PicoQuant ptu/pt3 FLIM image files

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

Toolbox for post-correlation cryo-CLEM workflow developed at Chlanda Lab, Heidelberg University.

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