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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.
- GitHub: https://github.com/topics/imagej
- Wikipedia: https://en.wikipedia.org/wiki/ImageJ
- Repo: https://github.com/imagej/imagej
- Aliases: fiji, fiji-plugin,
- Last updated: 2024-12-17 00:14:42 UTC
- JSON Representation
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: 03 Jan 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: 25 Oct 2024
https://github.com/qupath/qupath
QuPath - Open-source bioimage analysis for research
bioimage-analysis bioimage-informatics cell-analysis cell-segmentation computational-pathology digital-pathology groovy histology image-processing imagej javafx machine-learning opencv pathology tissue-microarray-analysis whole-slide-imaging
Last synced: 02 Jan 2025
https://github.com/cgohlke/tifffile
Read and write TIFF files
format-reader image imagej life-sciences-image numpy ome-tiff python tiff whole-slide-imaging zarr
Last synced: 02 Jan 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: 14 Nov 2024
https://github.com/cgohlke/roifile
Read and write ImageJ ROI format
format-reader imagej python region-of-interest
Last synced: 28 Dec 2024
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: 02 Dec 2024
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: 14 Nov 2024
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: 08 Nov 2024
https://github.com/morphonets/SNT
The ImageJ framework for quantification of neuronal anatomy
imagej imagej2 janelia neuroanatomy-toolbox neurons neuroscience scijava
Last synced: 14 Nov 2024
https://github.com/bockp/Edge-Detection-project
Tiny Image in Javascript - Edge Detection Algorithms
algorithm benchmark canny-edge-detection edge-detection edge-detection-algorithms imagej javascript laplace sobel webgl
Last synced: 20 Nov 2024
https://github.com/ij-plugins/ijp-color
Plugins for ImageJ - color space conversions and color calibration
ijp-color imagej sbt-imagej scala
Last synced: 14 Nov 2024
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: 16 Nov 2024
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: 14 Nov 2024
https://github.com/UU-cellbiology/ZstackDepthColorCode
Z-stack Depth Colorcode ImageJ FIJI plugin
colorcode fiji fiji-plugin imagej imagej-plugin microscopy utrecht-university
Last synced: 14 Nov 2024
https://github.com/bonej-org/BoneJ2
Plugins for bone image analysis
fiji-plugin image-analysis image-processing imagej imagej-plugins java-8 maven-multimodule scientific-computing skeletal-biology travis-ci
Last synced: 14 Nov 2024
https://github.com/dahie/imageflow
Visual ImageJ Macro editing in a node-base editor featuring ImageJ
Last synced: 12 Nov 2024
https://github.com/imagingbook/imagingbook-calibrate
Java/ImageJ implementation of Zhang's camera calibration method
burger-burge camera-calibration imagej java
Last synced: 11 Oct 2024
https://github.com/quantixed/imagej-macros
quantixed FIJI update site
figure-maker fiji fiji-macro imagej imagej-macros tiff
Last synced: 13 Nov 2024
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: 14 Nov 2024
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: 11 Oct 2024
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: 03 Dec 2024
https://github.com/mianalysis/mia
Modular, object-based analysis for ImageJ/Fiji
fiji-plugin image-analysis image-processing imagej modular
Last synced: 14 Nov 2024
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: 14 Nov 2024
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 segment-anything segment-anything-model whole-slide-image
Last synced: 19 Nov 2024
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: 16 Nov 2024
https://github.com/quantixed/cellmigration
Analysis of cell migration in Igor Pro
cell-migration igor imagej tracking
Last synced: 13 Nov 2024
https://github.com/quantixed/CellMigration
Analysis of cell migration in Igor Pro
cell-migration igor imagej tracking
Last synced: 14 Nov 2024
https://github.com/spatialsimulator/XitoSBML
XitoSBML - the spatial SBML plugin for ImageJ
fiji imagej sbml spatial-sbml-plugin systems-biology
Last synced: 14 Nov 2024
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: 14 Nov 2024
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: 07 Nov 2024
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: 15 Nov 2024
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: 03 Dec 2024
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: 17 Dec 2024
https://github.com/multi-template-matching/multi-template-matching
Homepage of the project
fiji imagej microscopy object-detection opencv
Last synced: 25 Dec 2024
https://github.com/hadim/mm_scripts
A collection of scripts related to Micro-Manager.
fiji imagej imagej2 java micro-manager microscope
Last synced: 23 Dec 2024
https://github.com/scijava/batch-processor
A Batch Processor for SciJava
batch-processor image-processing imagej scijava
Last synced: 07 Dec 2024
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: 31 Dec 2024
https://github.com/imagej/imagej-command-archetype
Maven archetype for a SciJava/ImageJ2 Command
imagej maven-archetype scijava
Last synced: 09 Nov 2024
https://github.com/imagingbook/imagingbook-maven-demo-project
imagingbook-maven-demo-project
imagej imagingbook java plugins
Last synced: 15 Nov 2024
https://github.com/biologytools/imagej.net
ImageJ Control using C# and IKVM.
Last synced: 03 Dec 2024
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: 03 Dec 2024
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: 17 Dec 2024
https://github.com/imagej/imagej-benchmarks
JMH-based benchmarks for projects of https://github.com/imagej/.
Last synced: 02 Jan 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: 22 Nov 2024
https://github.com/syncrossus/ijcarddetector
A playing card detection plugin for ImageJ.
binarization canny canny-edge-detection connected-components edge-detection gaussian-filter hough-transform hysteresis image-processing imagej imagej-plugins java otsu pattern-matching pattern-recognition playing-cards sobel template-matching
Last synced: 10 Nov 2024
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: 19 Dec 2024
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: 11 Nov 2024
https://github.com/quantixed/ferritag
FerriTag modelling and spatial analysis in Igor Pro
igor imagej imod spatial-analysis
Last synced: 13 Nov 2024
https://github.com/jefferis/scanimage
read and analyse 2 photon images from ScanImage
2-photon image-processing imagej r scanimage
Last synced: 15 Nov 2024
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 qupath
Last synced: 03 Dec 2024
https://github.com/dermatologist/skinhelpdesk
:information_desk_person: Image Analytics Library for Dermatology
dermatology image-processing imagej
Last synced: 15 Dec 2024
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: 13 Nov 2024
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: 12 Nov 2024
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: 27 Dec 2024
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: 13 Nov 2024
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: 13 Nov 2024
https://github.com/dlegland/ij-game-of-life
Conway's Game of Life implemented as a plugin for ImageJ
Last synced: 14 Nov 2024
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: 11 Nov 2024
https://github.com/quantixed/misseg
Chromosome missegregation analysis tools for Igor Pro, R and ImageJ
Last synced: 13 Nov 2024
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
Last synced: 15 Nov 2024
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: 11 Nov 2024
https://github.com/laulauthom/objectdetectionexamples-imagej.js
Example of ImageJ macros for object-localization
imagej imagej-js imagej-macro object-detection
Last synced: 15 Nov 2024
https://github.com/imcf/imcf-fiji-toolbars
:coffee: :microscope: :symbols: Fiji Action Bars provided by the IMCF.
fiji image-processing imagej imageprocessing
Last synced: 11 Nov 2024
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: 15 Nov 2024
https://github.com/sciviews/rimagej
R interface to ImageJ
image-classification image-processing image-segmentation imagej r r-package
Last synced: 24 Nov 2024
https://github.com/dermatologist/dit4ij
DIT4IJ - Dermatology Image Tagger for ImageJ
Last synced: 15 Dec 2024
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: 15 Dec 2024