My Top FIJI Plugins and Resources for Image Processing and Analysis

I love FIJI. It’s capabilities and talented community of developers are incredible. In the name of democratizing imaging software for the masses and generating repeatable, reliable image processing pipelines, I try to use it for the majority of my image processing and analysis needs. But it’s taken me a while to get to that point. To save you some time, I’ve compiled a bunch of useful resources and plugins I have found over the course of my studies


FIJI Download:

Open Imaging Community Forum:

Scripting Commands:

Image Analysis crash course Youtube Playlists:

Cool thread on using FFT to blend images from York and Prerbisch:

FIJI Scripting Workshop:

4D Data Analysis with Python / ImgLib2:


This is not an exhaustive list, but I will update as I find more useful plugins.

  • Bioformats – easy importing of proprietary image formats
  • Neurocyto LUTs – More color maps than you know what to do with
  • CLIJ – GPU-accelerated image processing in FIJI | Java-OpenCL bridge. works like a dream for processing large 3D data sets (z-stacks, time series, etc.).
  • 3D ImageJ Suite – Tons of useful tools and filtering methods for 3D processing
  • BigStitcher – if you do a lot of large tiling and volume registration, you need this.
  • ClearVolume – 3D data visualization. Lets you use custom LUTs, but is RAM intensive
  • HDF5 – for importing HDF5 files, e.g. large multivolume reconstructions
  • ImageJ-MATLAB – if you shuttle a lot of data between FIJI and Matlab, this helps
  • Deep Learning Image Processing
    • CSBDeep, TensorFlow, and Unet Segmentation
  • 3Dscript ( for install instructions) – Beautiful GPU-enabled 3D data visualization tool and animation generator. One of my current favorites.
  • MorphoLibJ – (under IJPB Plugins Update Site) TONS of useful filters and segmentation tools (like watershed segmentation!!!)

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