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An open API service indexing awesome lists of open source software.

ImageJ

ImageJ is an open source Java image processing program inspired by NIH Image. It runs on any computer with a Java 1.8 or later virtual machine. Downloadable distributions are available for Windows, Mac OS X and Linux. ImageJ has a strong, established user base, with thousands of plugins and macros for performing a wide variety of tasks.

Fiji is a “batteries-included” distribution of ImageJ, bundling many plugins which facilitate scientific image analysis.

https://github.com/image-py/imagepy

Image process framework based on plugin like imagej, it is esay to glue with scipy.ndimage, scikit-image, opencv, simpleitk, mayavi...and any libraries based on numpy

imagej opencv scikit-image simpleitk

Last synced: 15 May 2025

https://github.com/Image-Py/imagepy

Image process framework based on plugin like imagej, it is esay to glue with scipy.ndimage, scikit-image, opencv, simpleitk, mayavi...and any libraries based on numpy

imagej opencv scikit-image simpleitk

Last synced: 14 Mar 2025

https://github.com/ijpb/MorphoLibJ

Collection of mathematical morphology methods and plugins for ImageJ

3d-images fiji image-analysis image-processing imagej mathematical-morphology morpholibj

Last synced: 07 May 2025

https://github.com/imjoy-team/imagej.js

ImageJS--Image analysis in the browser with ImageJ

image-processing imagej

Last synced: 21 Jan 2026

https://github.com/cgohlke/roifile

Read and write ImageJ ROI format.

format-reader imagej python region-of-interest

Last synced: 21 Jan 2026

https://github.com/morphonets/SNT

The ImageJ framework for quantification of neuronal anatomy

fiji imagej imagej2 janelia neuroanatomy-toolbox neuron-reconstruction neurons neuroscience scijava

Last synced: 07 May 2025

https://github.com/mbalatsko/opencv-rolling-ball

Fully Ported to Python from ImageJ's Background Subtractor. Rolling ball and sliding paraboloid background subtraction algorithms.

background-subtraction image-processing imagej python3 rolling-ball sliding-paraboloid

Last synced: 11 Sep 2025

https://github.com/gtatters/thermimagej

ImageJ functions and macros for working with thermal image files

exiftool ffmpeg fiji fiji-macro heat-transfer imagej imagej-macro perl temperature-reading thermal-imaging

Last synced: 27 Jul 2025

https://github.com/thorstenwagner/ij-ridgedetection

Detect ridges / lines with imagej

detect-ridges fiji imagej

Last synced: 23 Jul 2025

https://github.com/gtatters/ThermImageJ

ImageJ functions and macros for working with thermal image files

exiftool ffmpeg fiji fiji-macro heat-transfer imagej imagej-macro perl temperature-reading thermal-imaging

Last synced: 07 May 2025

https://github.com/imagej/napari-imagej

Use ImageJ functionality from napari

fiji imagej java napari python

Last synced: 01 Aug 2025

https://github.com/tferr/scripts

:microscope::cocktail: Home of the ImageJ BAR: A collection of Broadly Applicable Routines for ImageJ

beanshell clojure groovy ijm image-analysis imagej imagej2 java jython microscopy python ruby scientific-workflows scripts-collection

Last synced: 14 Apr 2025

https://github.com/ij-plugins/ijp-color

Plugins for ImageJ - color space conversions and color calibration

ijp-color imagej sbt-imagej scala

Last synced: 02 Apr 2025

https://github.com/flika-org/flika

An interactive image processing program for biologists written in Python.

astrocytes biologists calcium fluorescence image-processing imagej microscopy neurons python

Last synced: 07 May 2025

https://github.com/dylanmuir/readimagejroi

Matlab function to import ROIs from ImageJ

imagej imagej2 import matlab roi

Last synced: 11 Apr 2025

https://github.com/imagingbook/imagingbook-public

Image processing software for textbooks by W. Burger & M. Burge

burger-burge digital-image-processing imagej imagej-plugins imagingbook java

Last synced: 29 Oct 2025

https://github.com/dahie/imageflow

Visual ImageJ Macro editing in a node-base editor featuring ImageJ

imagej java node-based-ui

Last synced: 09 Sep 2025

https://github.com/imagingbook/imagingbook-calibrate

Java/ImageJ implementation of Zhang's camera calibration method

burger-burge camera-calibration imagej java

Last synced: 29 Oct 2025

https://github.com/biologytools/bioimager

A .NET microscopy imaging application based on Bio library. Supports various microscopes by using imported libraries & GUI automation. Supports XInput game controllers to move stage, take images, run ImageJ macros on images or Bio C# scripts.

histology image-acquisition image-stacks imagej imagej-macro imaging micro-manager microscope microscope-control microscope-stage-controller microscopy plugin scripting whole-slide-imaging

Last synced: 10 Sep 2025

https://github.com/ropensci/ijtiff

An R Package for general purpose TIFF file I/O which plays nice with ImageJ

image-manipulation imagej peer-reviewed r r-package rstats tiff-files tiff-images

Last synced: 22 Oct 2025

https://github.com/emx77/ASI_MTF

Imagej macro to calculate the MTF based on a knife edge measurement

electron-microscopy image-analysis imagej imagej-macro imagej-plugins mtf point-spread-function x-ray-imaging

Last synced: 07 May 2025

https://github.com/ij-plugins/ijp-toolkit

ijp-toolkit general purpose plugins for ImageJ (also known as ij-plugins_toolkit)

ijp-toolkit image-analysis image-processing imagej sbt-imagej scala texture-synthesis

Last synced: 02 Apr 2025

https://github.com/biologytools/biogtk

A cross platform version of Bio library & program. Bio is a library & program for annotating, & editing various microscopy imaging formats using Bioformats supported images. including whole slide, pyramidal & series.

bio-formats biology cross-platform geojson gtk image-stacks imagej imagej-roi imagej-tiff microscopy omero openslide plugins qupath roi sam-2 segment-anything segment-anything-model whole-slide-image

Last synced: 15 May 2025

https://github.com/lukmuk/em-scalebartools

Fiji/ImageJ macros to quickly add a scale bar to an (electron microscopy) image.

electron-microscopy fiji imagej scalebar

Last synced: 07 May 2025

https://github.com/thorstenwagner/ij-nl-means

Non local means filter for ImageJ

denoising-images fiji image-denoising imagej

Last synced: 23 Jul 2025

https://github.com/mianalysis/mia

Modular, object-based analysis for ImageJ/Fiji

fiji-plugin image-analysis image-processing imagej modular

Last synced: 07 May 2025

https://github.com/thorstenwagner/ij-blob

ImageJ library to detect and analyse connected components (blobs) in binary images

binary-image component-analysis fiji image-analysis imagej imagej-plugins

Last synced: 23 Jul 2025

https://github.com/rocsg/fijirelax

FijiRelax: 3D+t multi-echo spin-echo sequences MRI analysis

image-processing imagej imagej-plugins java modeling mri relaxation-time

Last synced: 19 Oct 2025

https://github.com/quantixed/CellMigration

Analysis of cell migration in Igor Pro

cell-migration igor imagej tracking

Last synced: 07 May 2025

https://github.com/quantixed/cellmigration

Analysis of cell migration in Igor Pro

cell-migration igor imagej tracking

Last synced: 26 Nov 2025

https://github.com/ij-plugins/ijp-debayer2sx

Raw Bayer pattern to color image converters

bayer-filter bayer-pattern imagej imagej-plugins

Last synced: 07 Oct 2025

https://github.com/CellDynamics/QuimP

QuimP is software for tracking cellular shape changes and dynamic distributions of fluorescent reporters at the cell membrane.

cell imagej motility segmentation

Last synced: 07 May 2025

https://github.com/fmi-faim/fmi-ij2-plugins

A collection of ImageJ2 plugins for use with KNIME

bio-image-analysis image-processing imagej knime

Last synced: 16 Jan 2026

https://github.com/spatialsimulator/XitoSBML

XitoSBML - the spatial SBML plugin for ImageJ

fiji imagej sbml spatial-sbml-plugin systems-biology

Last synced: 07 May 2025

https://github.com/jpsacha/sbt-imagej

sbt-imagej is an SBT (Simmple Build Tool) plugin that that helps with development of ImageJ plugins

imagej imagej-plugins sbt-imagej sbt-plugin scala

Last synced: 11 Apr 2025

https://github.com/miura/yodosha-biasbook2025

『型で実践する生物画像解析　ImageJ・Python・napari』サポートサイト

bioimage-analysis fiji imagej japanese-language napari

Last synced: 22 Nov 2025

https://github.com/biologytools/imagej.net

ImageJ Control using C# and IKVM.

imagej

Last synced: 22 Aug 2025

https://github.com/laulauthom/fiji-roiclicktools

Fiji Toolbar tool with Roi that perform measurements, are added to Manager and auto next slice

clickable fiji ground-truth image-annotation imagej region-of-interest roi

Last synced: 02 Dec 2025

https://github.com/biologytools/biocore

Bio Library in .NET8. Bio is a library & program for annotating, & editing various microscopy imaging formats using Bioformats supported images. including whole slide, pyramidal & series.

bio-formats biology csv imagej imagej-roi microscopy ome roi whole-slide-image

Last synced: 23 Aug 2025

https://github.com/biologytools/bio

A .NET library & program for annotating, & editing various microscopy imaging formats using Bioformats supported images. including whole slide, pyramidal & series.

bio-formats biology csv imagej microscopy ome omero roi whole-slide-image

Last synced: 27 Jul 2025

https://github.com/hadim/fiji_maskrcnn

PROJECT MOVED TO https://github.com/hadim/maskflow-fiji

fiji imagej imaging microsopy neural-network segmentation semantic-segmentation tensorflow

Last synced: 04 Apr 2025

https://github.com/hadim/mm_scripts

A collection of scripts related to Micro-Manager.

fiji imagej imagej2 java micro-manager microscope

Last synced: 21 Jan 2026

https://github.com/biologytools/biolib

A GUI-less version of Bio .NET library for editing & annotating various microscopy image formats. Supports all bioformats supported images. Integrates with ImageJ, running ImageJ filters & macro functions.

geojson imagej imagej-macro imagej-roi omero omero-server qupath

Last synced: 17 Jun 2025

https://github.com/scijava/batch-processor

A Batch Processor for SciJava

batch-processor image-processing imagej scijava

Last synced: 19 Jan 2026

https://github.com/hereariim/napari-aphid

This directory contains all the elements and structure of the napari-aphid plugin

ilastik imagej napari-plugin python

Last synced: 03 Jul 2025

https://github.com/rsenft1/fish-ihc-colocalization-in-imagej

An ImageJ macro for 2D colocalization of IHC signals in ImageJ and counting RNAscope puncta within cells.

2d colocalization fiji fiji-macro imagej microscopy rnascope

Last synced: 01 Aug 2025

https://github.com/thorstenwagner/ij-nanotrackj

NanoTrackJ is an ImageJ/Fiji plugin to characterize the size of nanoparticles by its diffusion trajectories.

diffusion-coefficient diffusion-trajectories fiji-plugin hydrodynamic-diameter imagej nanoparticles size-distribution

Last synced: 23 Jul 2025

https://github.com/imagingbook/imagingbook-maven-demo-project

imagingbook-maven-demo-project

imagej imagingbook java plugins

Last synced: 13 Apr 2025

https://github.com/imagej/imagej-updater-tests

Docker-based test infrastructure for ImageJ Updater

docker imagej sandbox tests updater

Last synced: 18 Aug 2025

https://github.com/imcf/noisee

:microscope: NoiSee: An easy-to-use ImageJ macro for measuring SNR (signal-to-noise ratio) of light microscopes.

evaluation imagej imagej-macro measurements microscopy signal-to-noise

Last synced: 26 Feb 2025

https://github.com/ij-plugins/ijp-imageio

Read and write [ImageJ](http://rsb.info.nih.gov/ij/) images using Java ImageIO codes

ijp-imageio image-reader imageio imagej

Last synced: 02 Apr 2025

https://github.com/alessandrofelder/wallaby

ImageJ macros I use to semi-automatically process and analyse 2d microscopy images of cortical bone tissue. Could facilitate other 2d semi-automatic image analyses as well.

imagej macro microscopy semi-automatic

Last synced: 18 Jan 2026

https://github.com/imagej/imagej-command-archetype

Maven archetype for a SciJava/ImageJ2 Command

imagej maven-archetype scijava

Last synced: 08 Oct 2025

https://github.com/sedflix/active-contours-api-for-fiji-imagej

This is an easy to use active contours api for Fiji(ImageJ).

active-contour fiji fiji-plugin imagej imagej-plugins levelset

Last synced: 13 Oct 2025

https://github.com/jefferis/scanimage

read and analyse 2 photon images from ScanImage

2-photon image-processing imagej r scanimage

Last synced: 03 Aug 2025

https://github.com/christophmark/imagej-interactive-thresholding

ImageJ macros that automate the workflow of thresholding and analyzing the size and intensity of objects/regions in microscope images.

fiji fluorescence fluorescence-microscopy-imaging image-analysis image-processing image-segmentation imagej microscopy thresholding

Last synced: 02 Jan 2026

https://github.com/swharden/prairieview-quick-loader

ImageJ plugin to quickly load multiphoton imaging data from PrairieView folders

fluorescence fluorescence-microscopy-imaging imagej imagej-plugin microscopy multiphoton

Last synced: 21 Nov 2025

https://github.com/kinow/a4-to-a3

A Python script that uses Python libraries, ImageJ, and ImageMagick to automatically convert a scanned PDF with two A4 pages, into a single A3.

drawing figure-drawing image-stitching imagej imaging life-drawing

Last synced: 09 Jul 2025

https://github.com/imagej/imagej-benchmarks

JMH-based benchmarks for projects of https://github.com/imagej/.

benchmark imagej jmh

Last synced: 22 Feb 2025

https://github.com/quantixed/ferritag

FerriTag modelling and spatial analysis in Igor Pro

igor imagej imod spatial-analysis

Last synced: 01 Mar 2025

https://github.com/imcf/imcf-fiji-scripts

:wrench: :memo: :coffee: :microscope: Scripts for Fiji provided by the Imaging Core Facility, Biozentrum, University of Basel

facility fiji image-processing imagej imageprocessing

Last synced: 26 Apr 2025

https://github.com/ashkarin/rawimage

Read and write RAW images (or data arrays) without a headache.

image-processing imagej ndarray numpy raw-data raw-image readers writers

Last synced: 06 Nov 2025

https://github.com/dermatologist/skinhelpdesk

:information_desk_person: Image Analytics Library for Dermatology

dermatology image-processing imagej

Last synced: 02 Apr 2025

https://github.com/jumitti/skeletonanalyzer

Python script to facilitate the processing of data obtained with the AnalyzeSkeleton tool from Fiji/ImageJ

dataanalysis fiji imagej

Last synced: 28 Jun 2025

https://github.com/shermanlo77/modefilter

ImageJ plugin, Java and CuPy implementation of the mode filter and empirical null filter. The mode filter is an edge-preserving smoothing filter by taking the mode of the empirical density.

cuda cupy empirical-null fiji filter image-filter imagej jcuda mode-filter

Last synced: 27 Mar 2025

https://github.com/bruvellu/3d-tutorial

Tutorial on how to visualize 3D data in Fiji using built-in tools and 3Dscript

3d 3d-visualization 3dscript fiji imagej tutorial

Last synced: 13 Jan 2026

https://github.com/shermanlo77/oxwasp_phd

Code for the PhD thesis. The topic was on defect detection of 3D printing using x-rays. The repository includes an implementation of the mode filter and empirical null filter.

3d-printing applied-statistics computational-statistics cuda empirical-null imagej mode-filter statistics xray-projection

Last synced: 27 Mar 2025

https://github.com/arkitektio-apps/mikroj

Fiji/ImageJ with mikro

fiji imagej macros mikro

Last synced: 13 Sep 2025

https://github.com/dermatologist/java-ext

Java8 template for OpenFaaS that pulls Java modules from GitHub using JitPack.io

fhir h2oai imagej java8-template openfaas serverless

Last synced: 07 Sep 2025

https://github.com/quantixed/misseg

Chromosome missegregation analysis tools for Igor Pro, R and ImageJ

chromosome igor imagej

Last synced: 01 Mar 2025

https://github.com/richmit/imagej

ImageJ macros & tools for philately & raspberry pi camera

fiji image-processing imagej microscope-images microscopy philately raspberry-pi raspberry-pi-camera

Last synced: 02 Mar 2025

https://github.com/laulauthom/objectdetectionexamples-imagej.js

Example of ImageJ macros for object-localization

imagej imagej-js imagej-macro object-detection

Last synced: 04 Mar 2025

https://github.com/laulauthom/roigrouptable

Helper plugin providing a table to facilitate the setting of the names associated to the Roi-group integer indexes in Fiji

fiji imagej roi

Last synced: 04 Mar 2025

https://github.com/imcf/imcf-fiji-toolbars

:coffee: :microscope: :symbols: Fiji Action Bars provided by the IMCF.

fiji image-processing imagej imageprocessing

Last synced: 25 Jun 2025

https://github.com/bruvellu/cartography-tutorial

Tutorial on how to generate map projections using Blender Tissue Cartography

3d-visualization blender blender-tissue-cartography fiji ilastik imagej map-projections tissue-cartography tutorial

Last synced: 13 Jan 2026

https://github.com/peter-t-ruehr/checkpoint_converter

Converts any image stack to a Stratovan Checkpoint file (*.ckpt) keeping specimen names and voxel sizes.

biology botany checkpoint geometric-morphometrics image-stacks imagej imagej-macro micro-ct mri r tomography zoology

Last synced: 01 Jul 2025

https://github.com/imcf/jython-ome-model

:coffee: :snake: :microscope: :bookmark: :bookmark_tabs: A mavenized package of the Open Microscopy Environment "ome-model" Python module to be used in ImageJ2.

imagej imagej2 jython metadata ome ome-metadata ome-model python

Last synced: 26 Feb 2025

https://github.com/peter-t-ruehr/stack_cropping

ImageJ/Fiji macro that crops any given image stack without having to load it into memory first.

biology conversion cropping-images fiji histology image-macro image-stacks imagej material-science micro-ct mri tomography

Last synced: 21 Aug 2025

https://github.com/dermatologist/dit4ij

DIT4IJ - Dermatology Image Tagger for ImageJ

dermatology dicom imagej

Last synced: 05 Oct 2025

https://github.com/hilldr/hio_microinjection

This protocol describes the measurement of epithelial barrier permeability in real-time following pharmacologic treatment in human intestinal organoids using fluorescent microscopy and live cell microscopy

ggplot2 human-intestinal-organoids imagej latex-examples makefile organoid-microinjection protocol r reproducible-experiments reproducible-research tidyverse

Last synced: 13 Aug 2025

https://github.com/dlegland/ij-game-of-life

Conway's Game of Life implemented as a plugin for ImageJ

game-of-life imagej

Last synced: 04 Mar 2025

ImageJ Awesome Lists
awesome-biological-image-analysis 143
ImageJ Categories
Other 26 Image processing and segmentation 23 General image analysis software 18 Neuroscience 18 Plant science 10 Cell migration and particle tracking 9 Pathology 8 Electron and super resolution microscopy 7 Footnotes 6 Image restoration and quality assessment 6 Fluoresence in situ hybridization 5 Publications 5 Yeast imaging 4 Ecology 3 Microbiology 3 Mycology 2