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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: 2024-10-03 21:36:51 UTC
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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/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 Oct 2024

https://github.com/qupath/qupath

QuPath - Bioimage analysis & digital pathology

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: 09 Oct 2024

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: 30 Oct 2024

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: 03 Aug 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: 03 Aug 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: 03 Aug 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: 04 Aug 2024

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

Use ImageJ functionality from napari

fiji imagej java napari python

Last synced: 09 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: 03 Aug 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: 03 Aug 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: 03 Aug 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: 03 Aug 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/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: 03 Aug 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/lukmuk/em-scalebartools

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

electron-microscopy fiji imagej scalebar

Last synced: 03 Aug 2024

https://github.com/mianalysis/mia

Modular, object-based analysis for ImageJ/Fiji

fiji-plugin image-analysis image-processing imagej modular

Last synced: 03 Aug 2024

https://github.com/quantixed/CellMigration

Analysis of cell migration in Igor Pro

cell-migration igor imagej tracking

Last synced: 03 Aug 2024

https://github.com/spatialsimulator/XitoSBML

XitoSBML - the spatial SBML plugin for ImageJ

fiji imagej sbml spatial-sbml-plugin systems-biology

Last synced: 03 Aug 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/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: 03 Aug 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: 30 Oct 2024

https://github.com/hadim/mm_scripts

A collection of scripts related to Micro-Manager.

fiji imagej imagej2 java micro-manager microscope

Last synced: 30 Oct 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: 29 Oct 2024

https://github.com/multi-template-matching/multi-template-matching

Homepage of the project

fiji imagej microscopy object-detection opencv

Last synced: 06 Nov 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: 11 Oct 2024

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

Docker-based test infrastructure for ImageJ Updater

docker imagej sandbox tests updater

Last synced: 09 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: 15 Oct 2024

https://github.com/jefferis/scanimage

read and analyse 2 photon images from ScanImage

2-photon image-processing imagej r scanimage

Last synced: 11 Oct 2024

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

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

benchmark imagej jmh

Last synced: 09 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