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The U-Net Segmentation plugin for Fiji (ImageJ)

FIJI plugin for tracing of curvilinear structures in volumetric microscopy datasets

Plugins for bone image analysis

Z-stack Depth Colorcode ImageJ FIJI plugin

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

Curve tracing ImageJ plugin

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

ImageJ convenience layer for N5

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

browsing large volumetric data and shapes

Modular, object-based analysis for ImageJ/Fiji

Detection of Molecules plugin for ImageJ: SMLM 2D/3D localizations, drift and chromatic aberration correction, etc

ImgLib2 integration for ClearVolume

:microscope: 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.

ImageJ plugin reading PicoQuant ptu/pt3 FLIM image files

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

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

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 making kymographs of maximum or average intensity with wide lines, polylines, curves

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

Fiji plugins for qualitative image annotations + analysis workflows for image-classification and data-visualization

😎 Awesome lists about ImageJ Plugins!

This plugin segments and classify diffusion trajectories

playing with BigVolumeViewer LUTs/gamma/render

EVAnalyzer 1 - EV analyzing plugin for Fiji

Fiji/ImageJ plugin to annotate a labeled image

Fiji plugins for pQCT image analysis.